Composition and Methods for Producing Tobacco Plants and Products Having Increased Phenylalanine and Reduced Tobacco-Specific Nitrosamines (TSNAs)

ABSTRACT

The present disclosure provides approaches for reducing tobacco-specific nitrosamines (TSNAs) in tobacco. Some of these approaches include genetically engineering tobacco plants to increase one or more antioxidants, increase oxygen radicle absorbance capacity (ORAC), increase phenylalanine, or reduce nitrite. Also provided are methods and compositions for producing modified tobacco plants and tobacco products therefrom comprising reduced TSNAs.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of U.S. patent application Ser. No.16/372,833, filed Apr. 2, 2019, which claims priority to U.S.Provisional Application No. 62/652,092, filed on Apr. 3, 2018, and isincorporated by reference herein in its entirety.

INCORPORATION OF SEQUENCE LISTING

A sequence listing contained in the file named “P34599US02_SL.TXT” whichis 212,729 bytes (measured in MS-Windows®) and created on Jun. 1, 2022,comprises 73 sequences, is filed electronically herewith andincorporated by reference in its entirety.

FIELD

The present disclosure relates generally to methods for reducing tobaccospecific nitrosamines (TSNAs) comprising modulating the levels ofphenylalanine, antioxidants, nitrite, or antioxidant capacity. Alsoprovided are methods and compositions related to reducing or eliminatingTSNAs in cured leaf from tobacco plants and products, their developmentvia breeding or transgenic approaches, and production of tobaccoproducts from those tobacco plants.

BACKGROUND

Tobacco-specific nitrosamines (TSNAs), such as N-nitrosonornicotine(NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), can befound in smokeless tobacco; mainstream smoke; and side stream smoke ofcigarettes. It has been reported that air-cured and flue-cured tobaccocontain tobacco-specific nitrosamines. See, “Effect of Air-Curing on theChemical Composition of Tobacco”, Wiernik et al., Recent Adv. Tob. Sci,(1995), 21, pp. 39-80. According to Wiernik et al., TSNAs are notpresent in significant quantities in growing tobacco plants or fresh cuttobacco (green tobacco), but are formed during the curing process.Bacterial populations which reside on the tobacco leaf are stated tolargely cause the formation of nitrites from nitrate during curing andpossibly affect the direct catalysis of the nitrosation of secondaryamines at physiological pH values. The affected secondary amines includetobacco alkaloids, which form TSNAs when nitrosated.

Prior reports suggest several approaches to reduce TSNA levels. Forexample, WO2003/022081 proposed methods for reducing tobacco-specificnitrosamine (TSNA) content in cured tobacco by increasing the levels ofantioxidants in the tobacco prior to harvesting. Specifically,WO2003/022081 proposed root pruning of the tobacco plant prior toharvesting; severing the xylem tissue of the tobacco plant prior toharvesting; and administering antioxidants and/or chemicals whichincrease antioxidants to the tobacco plant after harvesting. Despiteprevious attempts and proposals, simpler, more uniform, more economicaland non-labor-intensive methods are desirable for reducing TSNA levelsin cured tobacco leaf. Here, the inventors address this need byproviding methods and compositions for reducing TSNAs by manipulatingantioxidant levels via, inter alia, modification of genes involved inantioxidant biosynthesis or regulation thereof.

SUMMARY

In one aspect, the present disclosure provides a method for reducing theamount of one or more Tobacco Specific Nitrosamines (TSNAs) in a curedleaf of a tobacco plant, the method comprising the steps of increasingthe amount of phenylalanine in the tobacco plant via a transgeneencoding or targeting a phenylalanine biosynthetic enzyme, a regulatorof phenylalanine biosynthesis, or a phenylalanine metabolic enzyme; andreducing the amount of one or more TSNAs in a cured leaf of the tobaccoplant or a tobacco product made from the cured tobacco leaf.

In one aspect, the present disclosure provides a method for reducing theamount of one or more TSNAs in a cured leaf of a tobacco plant, themethod comprising the steps of increasing the amount of phenylalanine inthe tobacco plant via a genetic modification in an endogenous gene,wherein the endogenous gene encodes a phenylalanine biosynthetic enzyme,a regulator of phenylalanine biosynthesis, or a phenylalanine metabolicenzyme; and reducing the amount of one or more TSNAs in a cured leaf ofthe tobacco plant or a tobacco product made from the cured tobacco leaf.

In one aspect, the present disclosure provides a method for increasingthe amount of one or more anthocyanins in a cured leaf of a tobaccoplant, the method comprising the steps of increasing the amount ofphenylalanine in the tobacco plant via a transgene encoding or targetinga phenylalanine biosynthetic enzyme, a regulator of phenylalaninebiosynthesis, or a phenylalanine metabolic enzyme; and increasing theamount of one or more anthocyanins in a cured leaf of the tobacco plantor a tobacco product made from the cured tobacco leaf.

In one aspect, the present disclosure provides a method for increasingthe amount of one or more anthocyanins in a cured leaf of a tobaccoplant, the method comprising the steps of increasing the amount ofphenylalanine in the tobacco plant via a genetic modification in anendogenous gene, wherein the endogenous gene encodes a phenylalaninebiosynthetic enzyme, a regulator of phenylalanine biosynthesis, or aphenylalanine metabolic enzyme; and increasing the amount of one or moreanthocyanins in a cured leaf of the tobacco plant or a tobacco productmade from the cured tobacco leaf.

In one aspect, the present disclosure provides a cured tobacco leaf of amodified tobacco plant, wherein the cured tobacco leaf comprises adecreased amount of one or more TSNAs and an increased amount of atleast one Chorismate Mutase-like polypeptide, wherein the decreased andincreased amounts are compared to an unmodified control tobacco plant.

In one aspect, the present disclosure provides a cured tobacco leaf of amodified tobacco plant, wherein the cured tobacco leaf comprises adecreased amount of one or more TSNAs and an increased amount ofphenylalanine, wherein the decreased and increased amounts are comparedto an unmodified control tobacco plant.

In one aspect, the present disclosure provides a cured tobacco leaf of amodified tobacco plant, wherein the cured tobacco leaf comprises adecreased amount of one or more TSNAs and an increased amount of one ormore phenylalanine biosynthetic enzymes, regulators of phenylalaninebiosynthesis, or phenylalanine metabolic enzymes, wherein the decreasedand increased amounts are compared to an unmodified control tobaccoplant.

BRIEF DESCRIPTION OF THE SEQUENCES

SEQ ID NOs: 1 to 23, 47 to 52, 64 to 65, and 68 to 70 are amino acidsequences of selected genes that are involved in antioxidant production.SEQ ID NOs: 24 to 46, 53 to 58, 66 to 67, and 71 to 73 are correspondingnucleic acid sequences that encode SEQ ID NOs: 1 to 23, 47 to 52, 64 to65, and 68 to 70, respectively. SEQ ID NOs: 59 to 63 are polynucleotidesencoding recombinant DNA molecules comprising cisgenic promoters, codingregions, and terminators.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 : TSNAs are formed when alkaloids nitrosinate in the presence ofnitrite.

FIG. 2 : Cloning of AtPAP1, NtAN2, and NtAN1 into 45-2-7 binary vector.

FIG. 3 : A control plant (left) exhibits a similar growth profilecompared AtPAP1 overexpression plants (right). AtPAP1 plants exhibit apurple color due to anthocyanin accumulation.

FIG. 4A: total TSNAs are reduced in AtPAP1 overexpression lines. FIG.4B: NNN levels are reduced in AtPAP1 overexpression lines compared tocontrols. FIG. 4C: NNK levels are reduced in AtPAP1 overexpression linescompared to controls. FIG. 4D: NAB levels are reduced in AtPAP1overexpression lines compared to controls. FIG. 4E: NAT levels arereduced in AtPAP1 overexpression lines compared to controls.

FIG. 5 : Oxygen radical absorbance capacity (ORAC) values in AtPAP1overexpression plants are increased compared to controls.

FIG. 6A: Nitrite levels in AtPAP1 overexpression plants are reducedcompared to controls. FIG. 6B: Nitrate levels in AtPAP1 overexpressionplants are not consistently different from controls.

FIG. 7 : HCT and HQT function in the biosynthetic pathway of ChlorogenicAcid.

FIG. 8 : Chlorogenic Acid levels are reduced in 3 of 4 HQT RNAi linesbut not in HCT RNAi lines.

FIG. 9 : Total TSNAs are increased in the 3 HQT RNAi lines withdecreased Chlorogenic Acid levels.

FIG. 10 : Accumulation of Chlorogenic Acid is inversely correlated withTSNA levels. A negative correlation is observed between CGA levels andtotal TSNA levels as shown in Table 4 and FIG. 10A. This correlation isalso observed between CGA levels and individual TSNAs NNN (FIG. 10B),NNK (FIG. 10C), NAB (FIG. 10D), and NAA (FIG. 10E).

FIG. 11 : The phenylpropanoid pathway can be targeted to reduce TSNAlevels in tobacco by increasing antioxidant levels.

FIG. 12 : The phenylpropanoid pathway leads to the biosynthesis of manyantioxidants.

FIG. 13 : Overexpression of AtPAP1 in TN90 and Narrow Leaf Madole (NLM)results in increased antioxidant capacity as measured using a FRAPassay. Measurements from leaves from at least five plants are averagedtogether for unmodified TN90 and NLM, two independent linesoverexpressing AtPAP1 in TN90, and two independent lines overexpressingAtPAP1 in NLM are tested using a FRAP assay. Both independent linesoverexpressing AtPAP1 in TN90 exhibit a highly significant increase inaverage antioxidant capacity (P<0.01) compared to unmodified TN90plants. Both independent lines overexpressing AtPAP1 in NLM exhibit ahighly significant increase in average antioxidant capacity (P<0.01)compared to unmodified NLM plants.

FIG. 14 : Overexpression of NtAN2 (SEQ ID NO: 30) in NLM results inincreased antioxidant capacity as measured using a FRAP assay.Greenhouse grown, individually tested T0 plants overexpressing NtAN2show increased antioxidant capacity compared to the average antioxidantcapacity determined for at least five unmodified NLM plants.

FIG. 15 : Overexpression of NtAN1a (SEQ ID NO: 28) in NLM results inincreased antioxidant capacity as measured using a FRAP assay.Greenhouse grown, individually tested T0 plants overexpressing NtAN1ashow increased antioxidant capacity compared to the average antioxidantcapacity determined for at least five unmodified NLM plants.

FIG. 16 : Overexpression of NtDFR (SEQ ID NO: 37) in NLM results inincreased antioxidant capacity as measured using a FRAP assay.Greenhouse grown, individually tested T₀ plants overexpressing NtDFRshow increased antioxidant capacity compared to the average antioxidantcapacity determined for at least five unmodified NLM plants.

FIG. 17 : Overexpression of NtJAF13 (SEQ ID NO: 33) in NLM results inincreased antioxidant capacity as measured using a FRAP assay.Greenhouse grown, individually tested T₀ plants overexpressing NtJAF13show increased antioxidant capacity compared to the average antioxidantcapacity determined for at least five unmodified NLM plants.

FIG. 18 : Overexpression of NtMYB3 (SEQ ID NO: 36) in NLM results inincreased antioxidant capacity as measured using a FRAP assay.Greenhouse grown, individually tested T₀ plants overexpressing NtMYB3show increased antioxidant capacity compared to the average antioxidantcapacity determined for at least five unmodified NLM plants.

FIG. 19 : Overexpression of NtMYB3 (SEQ ID NO: 36) in NLM results intobacco plants with normal leaf color in T₀ plants grown in thegreenhouse.

FIG. 20 : Overview of the Shikimate pathway for the biosynthesis ofaromatic amino acids. Based on FIG. 3 of Tzin and Galili., MolecularPlant, 3(6):956-972 (2010) (incorporated by reference herein in itsentirety).

FIG. 21 : Phenylalanine feeding of AtPAP1 overexpressing plantsincreases antioxidant capacity as determined by FRAP analysis. NLM andplants from two independent T₂ AtPAP1 overexpressing lines are treatedwith 0 mM, 2 mM, or 4 mM phenylalanine. Leaves are harvested andantioxidant capacity is determined using a FRAP analysis. In the controland both AtPAP1 overexpressing lines, antioxidant capacity increaseswith phenylalanine feeding.

FIG. 22 : Total TSNA accumulation measured in parts per million (PPM) indark tobacco leaves. PAP1 and MYB2 are expressed in both NLM darktobacco and NLM SRC dark tobacco. Plants are grown in the field andharvested using normal techniques before being cured. A) Total TSNAaccumulation in fire cured leaves. B) Total TSNA accumulation in aircured leaves. Error bars represent standard error.

FIG. 23 : Specific TSNA accumulation measured in PPM in dark tobaccoleaves that are fire cured. PAP1 and MYB2 are expressed in both NLM darktobacco and NLM SRC dark tobacco. Plants are grown in the field andharvested using normal techniques before being fire cured. A) NNNaccumulation in fire cured leaves. B) NNK accumulation in fire curedleaves. Error bars represent standard error.

FIG. 24 : Specific TSNA accumulation measured in PPM in dark tobaccoleaves that are fire cured. PAP1 and MYB2 are expressed in both NLM darktobacco and NLM SRC dark tobacco. Plants are grown in the field andharvested using normal techniques before being fire cured. A) NATaccumulation in fire cured leaves. B) NAB accumulation in fire curedleaves. Error bars represent standard error.

FIG. 25 : Specific TSNA accumulation measured in PPM in dark tobaccoleaves that are air cured. PAP1 and MYB2 are expressed in both NLM darktobacco and NLM SRC dark tobacco. Plants are grown in the field andharvested using normal techniques before being air cured. A) NNNaccumulation in air cured leaves. B) NNK accumulation in air curedleaves. Error bars represent standard error.

FIG. 26 : Specific TSNA accumulation measured in PPM in dark tobaccoleaves that are air cured. PAP1 and MYB2 are expressed in both NLM darktobacco and NLM SRC dark tobacco. Plants are grown in the field andharvested using normal techniques before being air cured. A) NATaccumulation in air cured leaves. B) NAB accumulation in air curedleaves. Error bars represent standard error.

FIG. 27 : Total alkaloid accumulation measured as percent per gram indark tobacco leaves that are fire cured. PAP1 and MYB2 are expressed inboth NLM dark tobacco and NLM SRC dark tobacco. Plants are grown in thefield and harvested using normal techniques before being fire cured. A)The amounts of nicotine measured as percent per gram. B) The amounts ofanatabine, anabasine, and nornicotine measured as percent per gram.Error bars represent standard error.

FIG. 28 : Total alkaloid accumulation measured as percent per gram indark tobacco leaves that are air cured. PAP1 and MYB2 are expressed inboth NLM dark tobacco and NLM SRC dark tobacco. Plants are grown in thefield and harvested using normal techniques before being air cured. A)The amounts of nicotine measured as percent per gram. B) The amounts ofanatabine, anabasine, and nornicotine measured as percent per gram.Error bars represent standard error.

DETAILED DESCRIPTION

Unless defined otherwise, technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art. One skilled in the art will recognize many methods can be usedin the practice of the present disclosure. Indeed, the presentdisclosure is in no way limited to the methods and materials described.For purposes of the present disclosure, the following terms are definedbelow.

Any references cited herein, including, e.g., all patents, publishedpatent applications, and non-patent publications, are incorporated byreference in their entirety.

As used herein, the singular form “a,” “an,” and “the” include pluralreferences unless the context clearly dictates otherwise. For example,the term “a compound” or “at least one compound” may include a pluralityof compounds, including mixtures thereof.

The term “about” is used herein to mean approximately, roughly, around,or in the region of. When the term “about” is used in conjunction with anumber or numerical range, it modifies that number or range by extendingthe boundaries above and below the numerical values set forth by 10%.

As used herein, a tobacco plant can be from any plant from the Nicotianatabacum genus including, but not limited to Nicotiana tabacum tabacum;Nicotiana tabacum amplexicaulis PI 271989; Nicotiana tabacum benthamianaPI 555478; Nicotiana tabacum bigelovii PI 555485; Nicotiana tabacumdebneyi; Nicotiana tabacum excelsior PI 224063; Nicotiana tabacumglutinosa PI 555507; Nicotiana tabacum goodspeedii PI 241012; Nicotianatabacum gossei PI 230953; Nicotiana tabacum hesperis PI 271991;Nicotiana tabacum knightiana PI 555527; Nicotiana tabacum maritima PI555535; Nicotiana tabacum megalosiphon PI 555536; Nicotiana tabacumnudicaulis PI 555540; Nicotiana tabacum paniculata PI 555545; Nicotianatabacum plumbaginifolia PI 555548; Nicotiana tabacum repanda PI 555552;Nicotiana tabacum rustica; Nicotiana tabacum suaveolens PI 230960;Nicotiana tabacum sylvestris PI 555569; Nicotiana tabacum tomentosa PI266379; Nicotiana tabacum tomentosiformis; and Nicotiana tabacumtrigonophylla PI 555572.

In one aspect, this disclosure provides methods and compositions relatedto modified tobacco plants, seeds, plant components, plant cells, andproducts made from modified tobacco plants, seeds, plant parts, andplant cells. In one aspect, a modified seed provided herein gives riseto a modified plant provided herein. In one aspect, a modified plant,seed, plant component, plant cell, or plant genome provided hereincomprises a recombinant DNA construct provided herein. In anotheraspect, cured tobacco material or tobacco products provided hereincomprise modified tobacco plants, plant components, plant cells, orplant genomes provided herein.

As used herein, “modified” refers to plants, seeds, plant components,plant cells, and plant genomes that have been subjected to mutagenesis,genome editing, genetic transformation, or a combination thereof.

In one aspect, the present disclosure provides a modified tobacco plantcapable of producing cured tobacco leaf comprising a decreased amount ofone or more tobacco-specific nitrosamines (TSNAs) and further comprisingan increased amount of at least one Chorismate Mutase-like polypeptide,wherein the decreased and increased amounts are compared to anunmodified control tobacco plant. In one aspect, a reduced level of oneor more TSNAs is less than 50% of the level of the one or more TSNAs incured leaf from a control plant. In one aspect, a modified tobacco plantfurther comprises an increased amount of at least one polypeptide havingat least 80% homology to a sequence selected from the group consistingof SEQ ID Nos. 1 to 23, 47 to 52, and 64 to 65. In one aspect, amodified tobacco plant further comprises an increased amount of at leastone polypeptide having a sequence selected from the group consisting ofSEQ ID Nos. 1 to 23, 47 to 52, and 64 to 65.

In one aspect, the present disclosure provides a modified tobacco plantcapable of producing cured tobacco leaf comprising a decreased amount ofone or more TSNAs and an increased amount of phenylalanine, wherein thedecreased and increased amounts are compared to an unmodified controltobacco plant. In one aspect, a reduced level of one or more TSNAs isless than 50% of the level of the one or more TSNAs in cured leaf from acontrol plant. In one aspect, a modified tobacco plant further comprisesan increased amount of at least one polypeptide having at least 80%homology to a sequence selected from the group consisting of SEQ ID Nos.1 to 23, 47 to 52, and 64 to 65. In one aspect, a modified tobacco plantfurther comprises an increased amount of at least one polypeptide havinga sequence selected from the group consisting of SEQ ID Nos. 1 to 23, 47to 52, and 64 to 65.

In one aspect, the present disclosure provides a modified tobacco plantcapable of producing cured tobacco leaf comprising decreased amount ofone or more TSNAs and an increased amount of one or more phenylalaninebiosynthetic enzymes, regulators of phenylalanine biosynthesis, orphenylalanine metabolic enzymes, wherein said decreased and increasedamounts are compared to an unmodified control tobacco plant. In oneaspect, a reduced level of one or more TSNAs is less than 50% of thelevel of the one or more TSNAs in cured leaf from a control plant. Inone aspect, a modified tobacco plant further comprises an increasedamount of at least one polypeptide having at least 80% homology to asequence selected from the group consisting of SEQ ID Nos. 1 to 23, 47to 52, and 64 to 65. In one aspect, a modified tobacco plant furthercomprises an increased amount of at least one polypeptide having asequence selected from the group consisting of SEQ ID Nos. 1 to 23, 47to 52, and 64 to 65. In a further aspect, a regulator of phenylalaninebiosynthesis is a regulatory transcription factor.

In a further aspect, a transgene disclosed in the present disclosureencodes a Chorismate Mutase-like polypeptide. In a further aspect, atransgene disclosed in the present disclosure targets an endogenous geneencoding a Chorismate Mutase-like polypeptide. In a further aspect, aChorismate Mutase-like polypeptide has at least 80% homology to asequence from the group consisting of SEQ ID NOs: 68 to 70. In a furtheraspect, a Chorismate Mutase-like polypeptide has at least 85% homologyto a sequence from the group consisting of SEQ ID NOs: 68 to 70. In afurther aspect, a Chorismate Mutase-like polypeptide has at least 90%homology to a sequence from the group consisting of SEQ ID NOs: 68 to70. In a further aspect, a Chorismate Mutase-like polypeptide has atleast 91% homology to a sequence from the group consisting of SEQ IDNOs: 68 to 70. In a further aspect, a Chorismate Mutase-like polypeptidehas at least 92% homology to a sequence from the group consisting of SEQID NOs: 68 to 70. In a further aspect, a Chorismate Mutase-likepolypeptide has at least 93% homology to a sequence from the groupconsisting of SEQ ID NOs: 68 to 70. In a further aspect, a ChorismateMutase-like polypeptide has at least 94% homology to a sequence from thegroup consisting of SEQ ID NOs: 68 to 70. In a further aspect, aChorismate Mutase-like polypeptide has at least 95% homology to asequence from the group consisting of SEQ ID NOs: 68 to 70. In a furtheraspect, a Chorismate Mutase-like polypeptide has at least 96% homologyto a sequence from the group consisting of SEQ ID NOs: 68 to 70. In afurther aspect, a Chorismate Mutase-like polypeptide has at least 97%homology to a sequence from the group consisting of SEQ ID NOs: 68 to70. In a further aspect, a Chorismate Mutase-like polypeptide has atleast 98% homology to a sequence from the group consisting of SEQ IDNOs: 68 to 70. In a further aspect, a Chorismate Mutase-like polypeptidehas at least 99% homology to a sequence from the group consisting of SEQID NOs: 68 to 70. In a further aspect, a Chorismate Mutase-likepolypeptide has 100% homology to a sequence from the group consisting ofSEQ ID NOs: 68 to 70.

In a further aspect, a Chorismate Mutase-like polypeptide is encoded bya polynucleotide sequence having at least 80% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 85% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 90% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 91% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 92% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 93% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 94% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 95% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 96% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 97% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 98% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having at least 99% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73. In a furtheraspect, a Chorismate Mutase-like polypeptide is encoded by apolynucleotide sequence having 100% homology to a sequence selected fromthe group consisting of SEQ ID NOs: 71 to 73.

In one aspect, the present disclosure provides a modified tobacco plantcapable of producing cured tobacco leaf comprising a reduced level ofone or more tobacco-specific nitrosamines (TSNAs) and further comprisingan increased level of one or more antioxidants, wherein the reduced andincreased levels are compared to a control tobacco plant or cured leaffrom a control tobacco plant of the same variety when grown and curedunder comparable conditions. In one aspect, a reduced level of one ormore TSNAs is less than 50% of the level of the one or more TSNAs incured leaf from a control plant. In another aspect, a modified tobaccoplant further comprises an increased level of oxygen radical absorbancecapacity (ORAC) compared to a control tobacco plant when grown and curedunder comparable conditions. In a further aspect, cured leaf from amodified tobacco plant comprises a reduced level of nitrite compared tocured leaf from a control tobacco plant when grown and cured undercomparable conditions.

In another aspect, cured leaf from a modified tobacco plant comprises areduced level of total TSNAs compared to the cured leaf from a controltobacco plant when grown and cured under comparable conditions. In oneaspect, reduced one or more TSNAs are selected from the group consistingof N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) N′-nitrosoanabasine (NAB), and any combination thereof. In oneaspect, the level of total TSNAs or an individual TSNA is measured basedon a freeze-dried cured leaf sample using liquid chromatograph withtandem mass spectrometry (LC/MS/MS).

In one aspect, the present disclosure provides cured leaf from amodified tobacco plant comprising a reduced level of4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK) compared to curedleaf from a control tobacco plant of the same variety when grown andcured under comparable conditions. In one aspect, a reduced level of NNKis less than 50% of the level of the NNK in cured leaf from a controlplant. In one aspect, a modified tobacco plant or cured leaf from amodified tobacco plant further comprises an increased level of one ormore antioxidants compared to a control tobacco plant or cured tobaccoleaf from a control plant of the same variety when grown and cured undercomparable conditions. In another aspect, a modified tobacco plant orcured leaf from a modified tobacco plant further comprises an increasedlevel of oxygen radical absorbance capacity (ORAC) compared to a controltobacco or cured tobacco leaf from a control plant when grown and curedunder comparable conditions. In a further aspect, cured leaf from amodified tobacco plant comprises a reduced level of nitrite compared tocured leaf from a control tobacco plant when grown and cured undercomparable conditions. The role of nitrite in the formation isnitrosamines and TSNAs is linked to the reduction of nitrate by theactivity of bacteria during the curing process. Nitrite is believed togenerate nitrosating compounds which then react with secondary aminessuch as the tobacco alkaloids nicotine, nornicotine, anabasine, andanatabine to form TSNAs. Reducing the amount of nitrite and thereforethe nitrosation of tobacco alkaloids, the production of TSNAs can beprevented during the curing process.

In one aspect, a modified tobacco plant or cured leaf from a modifiedtobacco plant comprises an increased level of one or more anthocyaninsselected from the group consisting of Delphnidin, Cyanidin, Procyanidin,Prodelphinidin, Hesperetin, Perlargonidin, Peonidin, and Petunidin.

As used herein, “anthocyanins” are antioxidants that are derived fromthe aromatic amino acid phenylalanine. Biosynthesis of phenylalanine isthe first step in many different biosynthetic pathways leading tovarious downstream molecules, including flavonoids and anthocyanins,through the phenylpropanoid biosynthesis pathway. See, for example, FIG.2 of Rommens et al., Plant Biotechnology Journal, 6:870-886 (2008) andFIG. 9 of Tzin et al., The Plant Journal, 60:156-167 (2009).Phenylalanine is produced via the shikimate pathway which, through aseries of steps, transforms chorismate into phenylalanine, tyrosine, andtryptophan. Chorismate Mutase catalyzes a reaction transformingchorismate into prephenate. Prephenate is subsequently used to createboth tyrosine and phenylalanine. See, for example, FIG. 20 of thepresent disclosure which is based on FIG. 3 of Tzin and Galili.,Molecular Plant, 3(6):956-972 (2010) and FIG. 1 of Oliva et al.,Frontiers in Plant Science, 8:769 (2017).

In one aspect, a modified tobacco plant or cured leaf from a modifiedtobacco plant comprises an increased level of one or more antioxidantsselected from the group consisting of anthocyanidin, flavanone,flavanol, flavone, flavonol, isoflavone, hydroxybenzoic acid,hydroxycinnamic acid, ellagitannin, stibene, lignan, carotenoids, andglycyrrhzin.

In another aspect, a modified tobacco plant or cured leaf from amodified tobacco plant comprises an increased level of one or moreantioxidants selected from the group consisting of Delphnidin, Cyanidin,Procyanidin, Prodelphinidin, Hesperetin, Perlargonidin, Peonidin,Petunidin, Naringenin, Catechin, Epicatechin, Apigenin, Luteonin,Quercetin, Myricetin, Rutin, Genistein, Daidzein, Gallic acid, Vanillicacid, Protocatechuic acid, Ferunic acid, Cinnamic acid, Coumeric acid,Chlorogenic acid, Coffeic acid, ferulic acid, Sanguiin,

Resveratrol, Sesamin, Caretonoids, and Vitamin C.

Unless specified otherwise, measurements of alkaloid, polyamine, ornicotine levels (or another leaf chemistry or property characterization)or leaf grade index values mentioned herein for a tobacco plant,variety, cultivar, or line refer to average measurements, including, forexample, an average of multiple leaves of a single plant or an averagemeasurement from a population of tobacco plants from a single variety,cultivar, or line. Unless specified otherwise, the nicotine, alkaloid,or polyamine level (or another leaf chemistry or propertycharacterization) of a tobacco plant described here is measured 2 weeksafter topping in a pooled leaf sample collected from leaf number 3, 4,and 5 after topping. In another aspect, the nicotine, alkaloid, orpolyamine level (or another leaf chemistry or property characterization)of a tobacco plant is measured after topping in a leaf having thehighest level of nicotine, alkaloid, or polyamine (or another leafchemistry or property characterization). In an aspect, the nicotine,alkaloid, or polyamine level of a tobacco plant is measured aftertopping in leaf number 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30. Inanother aspect, the nicotine, alkaloid, or polyamine level (or anotherleaf chemistry or property characterization) of a tobacco plant ismeasured after topping in a pool of two or more leaves with consecutiveleaf numbers selected from the group consisting of leaf number 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, and 30. In another aspect, the nicotine,alkaloid, or polyamine level (or another leaf chemistry or propertycharacterization) of a tobacco plant is measured after topping in a leafwith a leaf number selected from the group consisting of between 1 and5, between 6 and 10, between 11 and 15, between 16 and 20, between 21and 25, and between 26 and 30. In another aspect, the nicotine,alkaloid, or polyamine level (or another leaf chemistry or propertycharacterization) of a tobacco plant is measured after topping in a poolof two or more leaves with leaf numbers selected from the groupconsisting of between 1 and 5, between 6 and 10, between 11 and 15,between 16 and 20, between 21 and 25, and between 26 and 30. In anotheraspect, the nicotine, alkaloid, or polyamine level (or another leafchemistry or property characterization) of a tobacco plant is measuredafter topping in a pool of three or more leaves with leaf numbersselected from the group consisting of between 1 and 5, between 6 and 10,between 11 and 15, between 16 and 20, between 21 and 25, and between 26and 30.

Alkaloid levels can be assayed by methods known in the art, for exampleby quantification based on gas-liquid chromatography, high performanceliquid chromatography, radio-immunoassays, and enzyme-linkedimmunosorbent assays. For example, nicotinic alkaloid levels can bemeasured by a GC-FID method based on CORESTA Recommended Method No. 7,1987 and ISO Standards (ISO TC 126N 394 E. See also Hibi et al., PlantPhysiology 100: 826-35 (1992) for a method using gas-liquidchromatography equipped with a capillary column and an FID detector.Unless specified otherwise, all alkaloid levels described here aremeasured using a method in accordance with CORESTA Method No 62,Determination of Nicotine in Tobacco and Tobacco Products by GasChromatographic Analysis, February 2005, and those defined in theCenters for Disease Control and Prevention's Protocol for Analysis ofNicotine, Total Moisture and pH in Smokeless Tobacco Products, aspublished in the Federal Register Vol. 64, No. 55 Mar. 23, 1999 (and asamended in Vol. 74, No. 4, Jan. 7, 2009).

Alternatively, tobacco total alkaloids can be measured using asegmented-flow colorimetric method developed for analysis of tobaccosamples as adapted by Skalar Instrument Co (West Chester, Pa.) anddescribed by Collins et al., Tobacco Science 13:79-81 (1969). In short,samples of tobacco are dried, ground, and extracted prior to analysis oftotal alkaloids and reducing sugars. The method then employs an aceticacid/methanol/water extraction and charcoal for decolorization.Determination of total alkaloids was based on the reaction of cyanogenchloride with nicotine alkaloids in the presence of an aromatic amine toform a colored complex which is measured at 460 nm. Unless specifiedotherwise, total alkaloid levels or nicotine levels shown herein are ona dry weight basis (e.g., percent total alkaloid or percent nicotine).

In one aspect, a modified tobacco plant or cured leaf from a modifiedtobacco plant comprises an antioxidant that is undetectable in thecontrol plant or leaf. In another aspect, a modified tobacco plant orcured leaf from a modified tobacco plant comprises an antioxidant thatdoes not exist in the control plant.

In another aspect, the present disclosure provides cured leaf from amodified tobacco plant comprising a reduced level of one or moretobacco-specific nitrosamines (TSNAs) and further comprising a reducedlevel of nitrite, wherein the reduced levels are compared to cured leaffrom a control tobacco plant of the same variety when grown and curedunder comparable conditions. In another aspect, a modified tobacco plantor cured leaf from a modified tobacco plant further comprises anincreased level of oxygen radical absorbance capacity (ORAC) compared tothe control tobacco plant or cured leaf from the control tobacco plantwhen grown and cured under comparable conditions.

In a further aspect, the present disclosure provides a modified tobaccoplant capable of producing cured leaf comprising a reduced level of oneor more tobacco-specific nitrosamines (TSNAs) and further comprising anincreased level of oxygen radical absorbance capacity (ORAC), andwherein the reduced and increased levels are compared to a controltobacco plant or cured leaf from a control tobacco plant of the samevariety when grown and cured under comparable conditions.

In one aspect, a reduced or increased level is within about 10%, withinabout 20%, within about 30%, within about 40%, within about 50%, withinabout 60%, within about 70%, within about 80%, within about 90%, withinabout 92%, within about 94%, within about 95%, within about 96%, withinabout 97%, within about 98%, or within about 99% lower or higher thanthe level in a control tobacco plant or cured leaf from a controltobacco plant when grown and cured under comparable conditions.

In another aspect, a reduced or increased level is within about 1 fold,within about 2 folds, within about 3 folds, within about 4 folds, withinabout 5 folds, within about 6 folds, within about 7 folds, within about8 folds, within about 9 folds, within about 10 folds, within about 15folds, within about 20 folds, within about 25 folds, or within about 30folds lower or higher than the level in a control tobacco plant or curedleaf from a control tobacco plant when grown and cured under comparableconditions.

In one aspect, a reduced or increased level is at least about 10%, atleast about 20%, at least about 30%, at least about 40%, at least about50%, at least about 60%, at least about 70%, at least about 80%, atleast about 90%, at least about 92%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, or atleast about 99% lower or higher than the level in a control tobaccoplant or cured leaf from a control tobacco plant when grown and curedunder comparable conditions.

In another aspect, a reduced or increased level is at least about 1fold, at least about 2 folds, at least about 3 folds, at least about 4folds, at least about 5 folds, at least about 6 folds, at least about 7folds, at least about 8 folds, at least about 9 folds, at least about 10folds, at least about 15 folds, at least about 20 folds, at least about25 folds, or at least about 30 folds lower or higher than the level in acontrol tobacco plant or cured leaf from a control tobacco plant whengrown and cured under comparable conditions.

In one aspect, a reduced or increased level is about 10%, about 20%,about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about90%, about 92%, about 94%, about 95%, about 96%, about 97%, about 98%,or about 99% lower or higher than the level in a control tobacco plantor cured leaf from a control tobacco plant when grown and cured undercomparable conditions.

In another aspect, a reduced or increased level is about 1 fold, about 2folds, about 3 folds, about 4 folds, about 5 folds, about 6 folds, about7 folds, about 8 folds, about 9 folds, about 10 folds, about 15 folds,about 20 folds, about 25 folds, or about 30 folds lower or higher thanthe level in a control tobacco plant or cured leaf from a controltobacco plant when grown and cured under comparable conditions.

In one aspect, a reduced or increased level is about 1-2 folds, about2-3 folds, about 3-4 folds, about 4-5 folds, about 5-6 folds, about 6-7folds, about 7-8 folds, about 8-9 folds, about 9-10 folds, about 10-15folds, about 15-20 folds, about 20-25 folds, about 25-30 folds, or about30-50 folds lower or higher than the level in a control tobacco plant orcured leaf from a control tobacco plant when grown and cured undercomparable conditions.

In another aspect, a reduced or increased level is about 1-10 folds,about 2-10 folds, about 3-10 folds, about 4-10 folds, about 5-10 folds,about 6-10 folds, about 7-10 folds, about 8-10 folds, about 9-10 folds,about 10-50 folds, about 15-50 folds, about 20-50 folds, about 25-50folds, or about 30-50 folds lower or higher than the level in a controltobacco plant or cured leaf from a control tobacco plant when grown andcured under comparable conditions.

In one aspect, cured leaf from a modified tobacco plant produces orcomprises less than 2, less than 1.8, less than 1.5, less than 1.2, lessthan 1.0, less than 0.8, less than 0.6, less than 0.4, less than 0.3,less than 0.2, less than 0.15, less than 0.1, or less than 0.05 ppmtotal TSNAs. In one aspect, cured leaf from a modified tobacco plantcomprises between 2 and 0.05, between 1.8 and 0.05, between 1.5 and0.05, between 1.2 and 0.05, between 1.0 and 0.05, between 0.8 and 0.05,between 0.6 and 0.05, between 0.4 and 0.05, between 0.3 and 0.05,between 0.2 and 0.05, between 0.15 and 0.05, or between 0.1 and 0.05 ppmtotal TSNAs. In one aspect, cured leaf from a modified tobacco plantcomprises between 2 and 0.05, between 1.8 and 0.1, between 1.5 and 0.15,between 1.2 and 0.2, between 1.0 and 0.3, between 0.8 and 0.4, orbetween 0.6 and 0.5 ppm total TSNAs.

In one aspect, cured leaf from a modified tobacco plant comprises orproduces less than 0.08 ppm NNK, wherein the level of the NNK level ismeasured based on a freeze-dried cured leaf sample using liquidchromatograph with tandem mass spectrometry (LC/MS/MS).

As used herein, “comparable conditions” refers to similar environmentalconditions, agronomic practices, and/or curing process for growing orcuring tobacco and making meaningful comparisons between two or moreplant genotypes so that neither environmental conditions nor agronomicpractices (including curing process) would contribute to, or explain,any differences observed between the two or more plant genotypes.Environmental conditions include, for example, light, temperature,water, humidity, and nutrition (e.g., nitrogen and phosphorus).Agronomic practices include, for example, seeding, clipping,undercutting, transplanting, topping, suckering, and curing. SeeChapters 4B and 4C of Tobacco, Production, Chemistry and Technology,Davis & Nielsen, eds., Blackwell Publishing, Oxford (1999), pp. 70-103.

As used herein, a “reduced” or “increased” level refers to astatistically significant change (reduction or increase) from areference point. As used herein, “statistically significant” refers to ap-value of less than 0.05, a p-value of less than 0.025, a p-value ofless than 0.01, or a p-value of less than 0.001 when using anappropriate measure of statistical significance (e.g., a one-tailed twosample t-test).

As used herein, a “control plant” refers to a comparator plant that isan unmodified tobacco plant of the same variety or a tobacco planthaving no transgene of interest, depending on the context or the purposeof the control plant. Control tobacco plants and plants of interest aregrown and cured under comparable conditions.

In one aspect, a modified tobacco plant provided herein has similar orhigher leaf yield compared to a control tobacco plant when grown andcured under comparable conditions. In an aspect, leaf yield is selectedfrom the group consisting of fresh yield, dry yield, and cured yield. Inone aspect, a modified tobacco plant provided herein produces a leafyield mass within about 50%, within about 45%, within about 40%, withinabout 35%, within about 30%, within about 25%, within about 20%, withinabout 15%, within about 10%, within about 5%, within about 4%, withinabout 3%, within about 2%, within about 1%, or within about 0.5%compared to a control tobacco plant when grown and cured undercomparable conditions. In another aspect, a modified tobacco plantprovided herein produces a leaf yield mass at least 0.25%, 0.5%, 1%,2.5%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%,or more than 100% higher compared to a control tobacco plant when grownand cured under comparable conditions. In another aspect, a modifiedtobacco plant provided herein produces a leaf yield mass 0.25%-100%,0.5%-100%, 1%-100%, 2.5%-100%, 5%-100%, 10%-100%, 15%-100%, 20%-100%,25%-100%, 30%-100%, 40%-100%, 50%-100%, 60%-100%, 70%-100%, 80%-100%,90%-100%, 100%-200%, 100%-175%, 100%-150%, 100%-125%, 0.25%-50%,0.5%-50%, 1%-50%, 2.5%-50%, 5%-50%, 10%-50%, 15%-50%, 20%-50%, 25%-50%,30%-50%, 40%-50%, 50%-200%, 50%-175%, 50%-150%, 50%-125%, 0.25%-25%,0.5%-25%, 1%-25%, 2.5%-25%, 5%-25%, 10%-25%, 15%-25%, 20%-25%, 25%-200%,25%-175%, 25%-150%, or 25%-125% higher compared to a control tobaccoplant when grown and cured under comparable conditions.

In one aspect, a modified tobacco plant provided herein has a similar orcomparable plant height compared to a control tobacco plant when grownand cured under comparable conditions. In one aspect, a modified tobaccoplant provided herein comprises a height within about 50%, within about45%, within about 40%, within about 35%, within about 30%, within about25%, within about 20%, within about 15%, within about 10%, within about5%, within about 4%, within about 3%, within about 2%, within about 1%,or within about 0.5% compared to a control tobacco plants when grown andcured under comparable conditions. In another aspect, a modified tobaccoplant provided herein comprises a height 0.25%, 0.5%, 1%, 2.5%, 5%, 10%,15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or more than100% taller compared to a control tobacco plant when grown and curedunder comparable conditions. In another aspect, a modified tobacco plantcomprises a height 0.25%-100%, 0.5%-100%, 1%-100%, 2.5%-100%, 5%-100%,10%-100%, 15%-100%, 20%-100%, 25%-100%, 30%-100%, 40%-100%, 50%-100%,60%-100%, 70%-100%, 80%-100%, 90%-100%, 100%-200%, 100%-175%, 100%-150%,100%-125%, 0.25%-50%, 0.5%-50%, 1%-50%, 2.5%-50%, 5%-50%, 10%-50%,15%-50%, 20%-50%, 25%-50%, 30%-50%, 40%-50%, 50%-200%, 50%-175%,50%-150%, 50%-125%, 0.25%-25%, 0.5%-25%, 1%-25%, 2.5%-25%, 5%-25%,10%-25%, 15%-25%, 20%-25%, 25%-200%, 25%-175%, 25%-150%, or 25%-125%taller compared to a control tobacco plant when grown and cured undercomparable conditions.

In one aspect, a modified tobacco plant provided herein produces leafthat has a similar or higher USDA grade index value compared to acontrol tobacco plant when grown and cured under comparable conditions.In one aspect, a modified tobacco plant provided herein produces leafwith a USDA grade index value within about 50%, within about 45%, withinabout 40%, within about 35%, within about 30%, within about 25%, withinabout 20%, within about 15%, within about 10%, within about 5%, withinabout 4%, within about 3%, within about 2%, within about 1%, or withinabout 0.5% compared to a control tobacco plant when grown and curedunder comparable conditions. In one aspect, a modified tobacco plantprovided herein is capable of producing leaf having a USDA grade indexvalue of 55 or more, 60 or more, 65 or more, 70 or more, 75 or more, 80or more, 85 or more, 90 or more, or 95 or more. In one aspect, amodified tobacco plant provided herein produces leaf with a USDA gradeindex value at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50,or more than 50 units higher compared to a control tobacco plant whengrown and cured under comparable conditions. In one aspect, a modifiedtobacco plant provided herein produces leaf with a USDA grade indexvalue 1-50, 1-45, 1-40, 1-35, 1-30, 1-29, 1-28, 1-27, 1-26, 1-25, 1-24,1-23, 1-22, 1-21, 1-20, 1-19, 1-18, 1-17, 1-16, 1-15, 1-14, 1-13, 1-12,1-11, 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-50, 2-45, 2-40,2-35, 2-30, 2-29, 2-28, 2-27, 2-26, 2-25, 2-24, 2-23, 2-22, 2-21, 2-20,2-19, 2-18, 2-17, 2-16, 2-15, 2-14, 2-13, 2-12, 2-11, 2-10, 2-9, 2-8,2-7, 2-6, 2-5, 2-4, 2-3, 3-50, 3-45, 3-40, 3-35, 3-30, 3-29, 3-28, 3-27,3-26, 3-25, 3-24, 3-23, 3-22, 3-21, 3-20, 3-19, 3-18, 3-17, 3-16, 3-15,3-14, 3-13, 3-12, 3-11, 3-10, 3-9, 3-8, 3-7, 3-6, 3-5, 3-4, 4-50, 4-45,4-40, 4-35, 4-30, 4-29, 4-28, 4-27, 4-26, 4-25, 4-24, 4-23, 4-22, 4-21,4-20, 4-19, 4-18, 4-17, 4-16, 4-15, 4-14, 4-13, 4-12, 4-11, 4-10, 4-9,4-8, 4-7, 4-6, 4-5, 5-50, 5-45, 5-40, 5-35, 5-30, 5-29, 5-28, 5-27,5-26, 5-25, 5-24, 5-23, 5-22, 5-21, 5-20, 5-19, 5-18, 5-17, 5-16, 5-15,5-14, 5-13, 5-12, 5-11, 5-10, 5-9, 5-8, 5-7, 5-6, 10-50, 10-40, 10-30,10-20, 20-50, 20-30, 20-40, or 20-30 units higher compared to a controltobacco plant when grown and cured under comparable conditions.

Tobacco grades are evaluated based on factors including, but not limitedto, the leaf stalk position, leaf size, leaf color, leaf uniformity andintegrity, ripeness, texture, elasticity, sheen (related with theintensity and the depth of coloration of the leaf as well as the shine),hygroscopicity (the faculty of the tobacco leaf to absorb and to retainthe ambient moisture), and green nuance or cast. Leaf grade can bedetermined, for example, using an Official Standard Grade published bythe Agricultural Marketing Service of the US Department of Agriculture(7 U.S.C. § 511). See, e.g., Official Standard Grades for Burley Tobacco(U.S. Type 31 and Foreign Type 93), effective Nov. 5, 1990 (55 F.R.40645); Official Standard Grades for Flue-Cured Tobacco (U.S. Types 11,12, 13, 14 and Foreign Type 92), effective Mar. 27, 1989 (54 F.R. 7925);Official Standard Grades for Pennsylvania Seedleaf Tobacco (U.S. Type41), effective Jan. 8, 1965 (29 F.R. 16854); Official Standard Gradesfor Ohio Cigar-Leaf Tobacco (U.S. Types 42, 43, and 44), effective Dec.8, 1963 (28 F.R. 11719 and 28 F.R. 11926); Official Standard Grades forWisconsin Cigar-Binder Tobacco (U.S. Types 54 and 55), effective Nov.20, 1969 (34 F.R. 17061); Official Standard Grades for WisconsinCigar-Binder Tobacco (U.S. Types 54 and 55), effective Nov. 20, 1969 (34F.R. 17061); Official Standard Grades for Georgia and FloridaShade-Grown Cigar-Wrapper Tobacco (U.S. Type 62), Effective April 1971.A USDA grade index value can be determined according to an industryaccepted grade index. See, e.g., Bowman et al, Tobacco Science,32:39-40(1988); Legacy Tobacco Document Library (Bates Document#523267826-523267833, Jul. 1, 1988, Memorandum on the Proposed BurleyTobacco Grade Index); and Miller et al., 1990, Tobacco Intern.,192:55-57 (all foregoing references are incorporated by inference intheir entirety). Alternatively, leaf grade can be determined viahyper-spectral imaging. See e.g., WO 2011/027315 (published on Mar. 10,2011, and incorporated by inference in its entirety).

In one aspect, a modified tobacco plant provided herein comprisestobacco leaf with reduced total TSNAs and further comprises one or moredesirable or enhanced properties, e.g., inhibited or reduced suckergrowth prior to or after topping. In one aspect, a modified plantprovided herein comprises fewer total suckers, smaller suckers, or bothcompared to a control plant lacking such modification when grown andcured under comparable conditions. In one aspect, smaller suckers of amodified plant provided herein comprise reduced mass, reduced length,reduced diameter, or a combination thereof compared to suckers of acontrol plant grown and cured under comparable conditions.

Unless specified otherwise, measurements of the level of total TSNAs,individual TSNA, total or individual alkaloid, total or individualantioxidant, leaf yield, or leaf grade index values mentioned herein forcured leaf from a tobacco plant, variety, cultivar, or line refer toaverage measurements, including, for example, an average of multipleleaves (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, or 20 or more leaves) of a single plant or an averagemeasurement from a population of tobacco plants from a single variety,cultivar, or line. A population of tobacco plants or a collection oftobacco leaf for determining an average measurement (e.g., fresh weightor leaf grading) can be of any size, for example, 5, 10, 15, 20, 25, 30,35, 40, or 50. Industry-accepted standard protocols are followed fordetermining average measurements or grade index values.

In one aspect, a modified tobacco plant or leaf provided here has asimilar leaf chemistry profile compared to a control plant when grownand cured under comparable conditions. Without being limiting, a leafchemistry profile can comprise the amount of alkaloids (e.g., nicotine,nornicotine, anabasine, anatabine), malic acid, and reducing sugars(e.g., dextrose), or a combination thereof in a tobacco plant or tobaccoleaf. In one aspect, a modified plant or leaf provided herein comprisesa total alkaloids level within about 90%, within about 80%, within about70%, within about 60%, within about 50%, within about 45%, within about40%, within about 35%, within about 30%, within about 25%, within about20%, within about 15%, within about 10%, within about 5%, within about4%, within about 3%, within about 2%, within about 1%, or within about0.5% of the total alkaloids level of a control plant when grown andcured under comparable conditions. In one aspect, a modified plant orleaf provided herein comprises a total alkaloids level that is reducedby at least 1%, at least 5%, at least 10%, at least 15%, at least 20%,at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, atleast 50%, at least 55%, at least 60%, at least 65%, at least 70%, atleast 75%, at least 80%, at least 85%, at least 90%, or at least 95%compared to a control plant when grown and cured under comparableconditions. In one aspect, a modified plant or leaf provided hereincomprises a nicotine level within about 90%, within about 80%, withinabout 70%, within about 60%, within about 50%, within about 45%, withinabout 40%, within about 35%, within about 30%, within about 25%, withinabout 20%, within about 15%, within about 10%, within about 5%, withinabout 4%, within about 3%, within about 2%, within about 1%, or withinabout 0.5% of the nicotine level of a control plant when grown and curedunder comparable conditions. In one aspect, a modified plant or leafprovided herein comprises a nornicotine level within about 50%, withinabout 45%, within about 40%, within about 35%, within about 30%, withinabout 25%, within about 20%, within about 15%, within about 10%, withinabout 5%, within about 4%, within about 3%, within about 2%, withinabout 1%, or within about 0.5% of the nornicotine level of a controlplant when grown and cured under comparable conditions. In one aspect, amodified plant or leaf provided herein comprises an anabasine levelwithin about 50%, within about 45%, within about 40%, within about 35%,within about 30%, within about 25%, within about 20%, within about 15%,within about 10%, within about 5%, within about 4%, within about 3%,within about 2%, within about 1%, or within about 0.5% of the anabasinelevel of a control plant when grown and cured under comparableconditions. In one aspect, a modified plant or leaf provided hereincomprises an anatabine level within about 50%, within about 45%, withinabout 40%, within about 35%, within about 30%, within about 25%, withinabout 20%, within about 15%, within about 10%, within about 5%, withinabout 4%, within about 3%, within about 2%, within about 1%, or withinabout 0.5% of the anatabine level of a control plant when grown andcured under comparable conditions. In one aspect, a modified plant orleaf provided herein comprises a malic acid level within about 50%,within about 45%, within about 40%, within about 35%, within about 30%,within about 25%, within about 20%, within about 15%, within about 10%,within about 5%, within about 4%, within about 3%, within about 2%,within about 1%, or within about 0.5% of the malic acid level of acontrol plant when grown and cured under comparable conditions. In oneaspect, a modified plant or leaf provided herein comprises a reducingsugars level within about 50%, within about 45%, within about 40%,within about 35%, within about 30%, within about 25%, within about 20%,within about 15%, within about 10%, within about 5%, within about 4%,within about 3%, within about 2%, within about 1%, or within about 0.5%of the reducing sugars level of a control plant when grown and curedunder comparable conditions. In one aspect, a modified plant or leafprovided herein comprises a dextrose level within about 50%, withinabout 45%, within about 40%, within about 35%, within about 30%, withinabout 25%, within about 20%, within about 15%, within about 10%, withinabout 5%, within about 4%, within about 3%, within about 2%, withinabout 1%, or within about 0.5% of the dextrose level of a control plantwhen grown and cured under comparable conditions.

In one aspect, a plant component provided herein includes, but is notlimited to, a leaf, a stem, a root, a seed, a flower, pollen, an anther,an ovule, a pedicel, a fruit, a meristem, a cotyledon, a hypocotyl, apod, an embryo, endosperm, an explant, a callus, a tissue culture, ashoot, a cell, and a protoplast. In further aspects, this disclosureprovides tobacco plant cells, tissues, and organs that are notreproductive material and do not mediate the natural reproduction of theplant. In another aspect, this disclosure also provides tobacco plantcells, tissues, and organs that are reproductive material and mediatethe natural reproduction of the plant. In another aspect, thisdisclosure provides tobacco plant cells, tissues, and organs that cannotmaintain themselves via photosynthesis. In another aspect, thisdisclosure provides somatic tobacco plant cells. Somatic cells, contraryto germline cells, do not mediate plant reproduction.

Provided cells, tissues and organs can be from seed, fruit, leaf,cotyledon, hypocotyl, meristem, embryos, endosperm, root, shoot, stem,pod, flower, inflorescence, stalk, pedicel, style, stigma, receptacle,petal, sepal, pollen, anther, filament, ovary, ovule, pericarp, phloem,and vascular tissue. In another aspect, this disclosure provides atobacco plant chloroplast. In a further aspect, this disclosure providesan epidermal cell, a stomata cell, a leaf hair (trichome), a root hair,or a storage root. In another aspect, this disclosure provides a tobaccoprotoplast.

Skilled artisans understand that tobacco plants naturally reproduce viaseeds, not via asexual reproduction or vegetative propagation. In oneaspect, this disclosure provides tobacco endosperm. In another aspect,this disclosure provides a tobacco endosperm cell. In a further aspect,this disclosure provides a male or female sterile tobacco plant, whichcannot reproduce without human intervention.

In one aspect, a modified plant, seed, plant part, or plant cellprovided herein comprises one or more non-naturally occurring mutations.In one aspect, a mutation provided herein suppresses TSNA levels incured leaf from a tobacco plant. Types of mutations provided hereininclude, for example, substitutions (point mutations), deletions,insertions, duplications, and inversions. Such mutations are desirablypresent in the coding region of a gene; however, mutations in a promoteror other regulatory region, an intron, an intron-exon boundary, or anuntranslated region of a gene may also be desirable.

In one aspect, a modified tobacco plant comprises one or more mutationsor modifications capable of providing the reduced level of one or moreTSNAs. In another aspect, one or more mutations are further capable ofproviding one or more traits selected from the group consisting of: i. areduced level of nitrite, ii. an increased level of oxygen radicleabsorbance capacity (ORAC), and iii. an increased level of one or moreantioxidants; wherein the reduced or increased level is compared to acontrol tobacco plant or cured leaf from a control tobacco plant whengrown and cured under comparable.

In one aspect, a mutation comprises a mutation type selected from thegroup consisting of an insertion, a deletion, an inversion, aduplication, a substitution, and a combination thereof.

In one aspect, a modified tobacco plant comprises one or more mutationsor modifications capable of activating one or more genes encoding abiosynthetic enzyme, a regulatory transcription factor, a transporter, acatabolic enzyme, or a combination thereof, for one or moreantioxidants. In another aspect, one or more mutations or modificationsare in one or more genes encoding a biosynthetic enzyme, a regulatorytranscription factor, a transporter, a catabolic enzyme, or acombination thereof, for one or more antioxidants selected from thegroup consisting of anthocyanidin, flavanone, flavanol, flavone,flavonol, isoflavone, hydroxybenzoic acid, hydroxycinnamic acid,ellagitannin, stibene, lignan, carotenoids, and glycyrrhzin. In afurther aspect, one or more mutations or modifications are in one ormore genes encoding a biosynthetic enzyme, a regulatory transcriptionfactor, a transporter, a catabolic enzyme, or a combination thereof, forone or more antioxidants selected from the group consisting ofDelphnidin, Cyanidin, Procyanidin, Prodelphinidin, Hesperetin,Perlargonidin, Peonidin, Petunidin, Naringenin, Catechin, Epicatechin,Apigenin, Luteonin, Quercetin, Myricetin, Rutin, Genistein, Daidzein,Gallic acid, Vanillic acid, Protocatechuic acid, Ferunic acid, Cinnamicacid, Coumeric acid, Chlorogenic acid, Coffeic acid, ferulic acid,Sanguiin, Resveratrol, Sesamin, Caretonoids, and Vitamin C.

In one aspect, a modified tobacco plant of the present disclosurecomprises tobacco leaves with increased levels of anthocyanins. In afurther aspect, a modified tobacco plant with increased levels ofanthocyanins further comprises leaves that have a purple or crimsonvisual appearance. In one aspect, a modified tobacco plant of thepresent disclosure comprises tobacco leaves with increased levels ofantioxidants and without increased levels of anthocyanins. In a furtheraspect, a modified tobacco plant comprising increased levels ofantioxidants and without increased levels of anthocyanins furthercomprises leaves with a visual appearance similar to an unmodifiedtobacco plant.

As used herein, a “biosynthetic enzyme” refers to a protein thatfunctions in the synthesis of phenylalanine, antioxidants, alkaloids,TSNAs, nitrite, nitrate, Chlorogenic Acid or other proteins affectingthe activity or stability of phenylalanine, antioxidants, alkaloids,TSNAs, nitrite, nitrate or Chlorogenic Acid. These proteins catalyzereactions that result in the transformation of one molecular structureinto another structure as part of a biosynthesis pathway. Exemplarybiosynthetic enzymes include but are not limited to Chorismate Mutase(CM), CM-like proteins, Prephenate Aminotransferase (PAT), PAT-likeproteins, Arogenate

Dehydratase (ADT), ADT-like proteins, Prephenate Dehydratase (PDT),PDT-like proteins, Aromatic Amino Acid Aminotransferase (AAAAT),AAAAT-like proteins, Anthocyanidin synthase2 (NtANS2),Dihyfroflavonol-4-reductase (NtDFR2), Shikimate O-hydroxycinnamoyltransferase (HCT), HCT-like proteins, Hydroxycinnamoyl CoA quinateTransferase (HQT), and HQT-like proteins. The activity of a biosyntheticenzyme effects the total concentration of different molecule speciesthat compose a biosynthetic pathway.

It is known that CM, PAT, ADT, PDT, and AAAAT play roles in themetabolism of aromatic amino acids, specifically, phenylalaninebiosynthesis. See Zhang et al. 2013, The Plant Journal 73:628-639; Li etal. 2015, Metabolic Engineering 32:1-11; Tzin et al. 2009, The PlantJournal 60:156-167; Rommens et al. 2008, Plant Biotechnology Journal6:870-886; Rippert et al. 2004, Plant Physiology 134:92-100; Oliva etal. 2017, Frontiers in Plant Science Vol 8, Article 769, Cho et al.2007, Journal of Biological Chemistry 282:42 20827-20835, Tzin andGalili 2010, The Arabidopsis Book e0132. 10.119/tab.0132 (each referenceis incorporated herein in its entirety). The consequences of CMdown-regulation have been studied is various plant species. For example,downregulation of CM in petunia results in a significant decrease inboth prephenate and phenylalanine. See Qian et al. 2019, NatureCommunications 10:15 (incorporated herein in its entirety) at FIG. 2C.Likewise, down regulation of ADT1 in petunia results in a significantdecrease in phenylalanine. See Yoo et al. 2013, Nature Communications4:2833(incorporated herein in its entirety) at FIG. 2C. Overexpressionof a dual function chorimstae mutase/prephrenate dehydratase gene fromArabidopisis results in increased levels of phenylalanine. See Tzin etal. 2009, The Plant Journal 60:156-167 at FIG. 3 . FIG. 20 outlines thephenylalanine metabolic pathway downstream of the Shikimate pathway.

As used herein, a “regulatory transcription factor” is a protein thatbinds a promoter element of a target gene to modulate the transcriptionof one or more genes involved in antioxidant biosynthesis, transport,catabolism, or other processes affecting the level of one or moreantioxidants. Exemplary regulatory transcription factors include AtPAP1,NtPAP1, NtMYB3-like, NtJAF13, and AtTTG1. A regulatory transcriptionfactor can bind DNA as part of a protein complex or individually. Aregulatory transcription factor can have a single target or multipletargets and can bind different targets with varying affinities. Theactivity of a regulatory transcription factor can be to activate,repress, or attenuate transcription from a target loci.

As used herein, a “transport protein” can be a transmembrane proteinthat actively or passively moves molecules across a biological membrane.A transport protein can aid in the movement of ions, small molecules ormacromolecules. A transport protein can be referred to as atransmembrane transporter, a transmembrane pump, an anion transportprotein, a cation transport protein, or an escort protein. Transportproteins can also facilitate the movement of molecules or proteins invesicles composed of biological membrane. A transport protein can beintegrated into a biological membrane. A Transport protein can beanchored to a biological membrane via different modifications such asbut not limited to myristolation, prenylation or palmitoylation.

In one aspect, a modified tobacco plant comprises one or more mutationsin a gene encoding a polypeptide having at least 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% identity to asequence selected from the group consisting of SEQ ID No. 1 to 23, 47 to52, 64 to 65, and 68 to 70. In another aspect, a modified tobacco plantcomprises one or more mutations in a gene comprise a coding sequencehaving at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%,98%, 99%, or 100% identity to a sequence selected from the groupconsisting of SEQ ID No. 24 to 46, 53 to 58, 66 to 67, and 71 to 73.

In one aspect, a modified plant, seed, plant component, plant cell, orplant genome provided herein comprises one or more transgenes. As usedherein, a “transgene” refers to a polynucleotide that has beentransferred into a genome by any method known in the art. In one aspect,a transgene is an exogenous polynucleotide. In one aspect, a transgeneis an endogenous polynucleotide that is integrated into a new genomiclocus where it is not normally found.

As used herein, “modified”, in the context of plants, seeds, plantcomponents, plant cells, and plant genomes, refers to a state containingchanges or variations from their natural or native state. For instance,a “native transcript” of a gene refers to an RNA transcript that isgenerated from an unmodified gene. Typically, a native transcript is asense transcript. Modified plants or seeds contain molecular changes intheir genetic materials, including either genetic or epigeneticmodifications. Typically, modified plants or seeds, or a parental orprogenitor line thereof, have been subjected to mutagenesis, genomeediting (e.g., without being limiting, via methods using site-specificnucleases), genetic transformation (e.g., without being limiting, viamethods of Agrobacterium transformation or microprojectile bombardment),or a combination thereof. In one aspect, a modified plant providedherein comprises no non-plant genetic material or sequences. In yetanother aspect, a modified plant provided herein comprises nointerspecies genetic material or sequences. In one aspect, thisdisclosure provides methods and compositions related to modified plants,seeds, plant components, plant cells, and products made from modifiedplants, seeds, plant parts, and plant cells. In one aspect, a modifiedseed provided herein gives rise to a modified plant provided herein. Inone aspect, a modified plant, seed, plant component, plant cell, orplant genome provided herein comprises a recombinant DNA construct orvector provided herein. In another aspect, a product provided hereincomprises a modified plant, plant component, plant cell, or plantchromosome or genome provided herein. The present disclosure providesmodified plants with desirable or enhanced properties, e.g., withoutbeing limiting, disease, insect, or pest tolerance (for example, virustolerance, bacteria tolerance, fungus tolerance, nematode tolerance,arthropod tolerance, gastropod tolerance); herbicide tolerance;environmental stress resistance; quality improvements such as yield,nutritional enhancements, environmental or stress tolerances; anydesirable changes in plant physiology, growth, development, morphologyor plant product(s) including starch production, modified oilsproduction, high oil production, modified fatty acid content, highprotein production, fruit ripening, enhanced animal and human nutrition,biopolymer production, pharmaceutical peptides and secretable peptidesproduction; improved processing traits; improved digestibility; lowraffinose; industrial enzyme production; improved flavor; nitrogenfixation; hybrid seed production; and fiber production.

As used herein, “genome editing” or editing refers to targetedmutagenesis, insertion, deletion, inversion, substitution, ortranslocation of a nucleotide sequence of interest in a genome using atargeted editing technique. A nucleotide sequence of interest can be ofany length, e.g., at least 1, at least 2, at least 3, at least 4, atleast 5, at least 6, at least 7, at least 8, at least 9, at least 10, atleast 15, at least 20, at least 25, at least 30, at least 35, at least40, at least 45, at least 50, at least 75, at least 100, at least 250,at least 500, at least 1000, at least 2500, at least 5000, at least10,000, or at least 25,000 nucleotides. As used herein, a “targetedediting technique” refers to any method, protocol, or technique thatallows the precise and/or targeted editing of a specific location in agenome (e.g., the editing is not random). Without being limiting, use ofa site-specific nuclease is one example of a targeted editing technique.Another non-limiting example of a targeted editing technique is the useof one or more tether guide Oligos (tgOligos). As used herein, a“targeted edit” refers to a targeted mutagenesis, insertion, deletion,inversion, or substitution caused by a targeted editing technique. Anucleotide sequence of interest can be an endogenous genomic sequence ora transgenic sequence.

In one aspect, a “targeted editing technique” refers to any method,protocol, or technique that allows the precise and/or targeted editingof a specific location in a genome (e.g., the editing is not random).Without being limiting, use of a site-specific nuclease is one exampleof a targeted editing technique.

In one aspect, a targeted editing technique is used to edit anendogenous locus or an endogenous gene. In another aspect, a targetedediting technique is used to edit a transgene. As used herein, an“endogenous gene” or a “native copy” of a gene refers to a gene thatoriginates from within a given organism, cell, tissue, genome, orchromosome. An “endogenous gene” or a “native copy” of a gene is a genethat was not previously modified by human action.

In one aspect, a modified tobacco plant described here comprises one ormore mutations are introduced via a system selected from the groupconsisting of chemical mutagenesis, irradiation mutagenesis, transposonmutagenesis, Agrobacterium-mediated transformation, a meganuclease, azinc-finger nuclease (ZFN), a transcription activator-like effectornuclease (TALEN), a clustered regularly-interspaced short palindromicrepeats (CRISPR)/Cas9 system, a CRISPR/Cpf1 system, a CRISPR/CasXsystem, a CRISPR/CasY system, a CRISPR/Csm1 system, and a combinationthereof (see, for example, U.S. Patent Application publication2017/0233756).

In one aspect, methods provided herein are capable of producing atobacco plant comprising a reduced level of one or more TSNAs usingmutagenesis. Mutagenesis methods include, without limitation, chemicalmutagenesis, for example, treatment of seeds with ethyl methylsulfate(EMS) (Hildering and Verkerk, In, The use of induced mutations in plantbreeding. Pergamon Press, pp. 317-320, 1965); or UV-irradiation, X-rays,electron beams, ion beams (e.g., carbon ion beam, helium ion beam, neonion beam), and fast neutron irradiation (see, for example, Verkerk,Neth. J. Agric. Sci. 19:197-203, 1971; Poehlman, Breeding Field Crops,Van Nostrand Reinhold, New York (3.sup.rd ed.), 1987; and Tanaka, J.Radiat. Res. 51:223-233, 2010); transposon tagging (Fedoroff et al.,1984; U.S. Pat. No. 4,732,856, 5,013,658); and T-DNA insertionmethodologies (Hoekema et al., 1983; U.S. Pat. No. 5,149,645).EMS-induced mutagenesis consists of chemically inducing random pointmutations over the length of a genome. Fast neutron mutagenesis consistsof exposing seeds to neutron bombardment which causes large deletionsthrough double stranded DNA breakage. Transposon tagging comprisesinserting a transposon within an endogenous gene to reduce or eliminateexpression of the gene.

In addition, a fast and automatable method for screening for chemicallyinduced mutations, TILLING (Targeting Induced Local Lesions In Genomes),using denaturing HPLC or selective endonuclease digestion of selectedPCR products is also applicable to the present disclosure. See, McCallumet al. (2000) Nat. Biotechnol. 18:455-457. Mutations that impact geneexpression or that interfere with the function of genes provided hereincan be determined using methods that are well known in the art.Insertional mutations in gene exons usually result in null-mutants.Mutations in conserved residues can be particularly effective ininhibiting the function of a protein.

The screening and selection of mutagenized tobacco plants can be throughany methodologies known to those having ordinary skill in the art.Examples of screening and selection methodologies include, but are notlimited to, Southern analysis, PCR amplification for detection of apolynucleotide, Northern blots, RNase protection, primer-extension,RT-PCR amplification for detecting RNA transcripts, Sanger sequencing,Next Generation sequencing technologies (e.g., Illumina, PacBio, IonTorrent, 454) enzymatic assays for detecting enzyme or ribozyme activityof polypeptides and polynucleotides, and protein gel electrophoresis,Western blots, immunoprecipitation, and enzyme-linked immunoassays todetect polypeptides. Other techniques such as in situ hybridization,enzyme staining, and immunostaining also can be used to detect thepresence or expression of polypeptides and/or polynucleotides. Methodsfor performing all of the referenced techniques are known.

In one aspect, a modified plant or plant genome provided herein ismutated or edited by a nuclease selected from the group consisting of ameganuclease, a zinc-finger nuclease (ZFN), a transcriptionactivator-like effector nuclease (TALEN), a CRISPR/Cas9 nuclease, aCRISPR/Cpf1 nuclease, a CRISPR/CasX nuclease, a CRISPR/CasY nuclease, ora CRISPR/Csm1 nuclease. As used herein, “editing” or “genome editing”refers to targeted mutagenesis of at least 1, at least 2, at least 3, atleast 4, at least 5, at least 6, at least 7, at least 8, at least 9, orat least 10 nucleotides of an endogenous plant genome nucleic acidsequence, or removal or replacement of an endogenous plant genomenucleic acid sequence. In one aspect, an edited nucleic acid sequenceprovided herein has at least 99.9%, at least 99.5%, at least 99%, atleast 98%, at least 97%, at least 96%, at least 95%, at least 94%, atleast 93%, at least 92%, at least 91%, at least 90%, at least 85%, atleast 80%, or at least 75% sequence identity with an endogenous nucleicacid sequence. In one aspect, an edited nucleic acid sequence providedherein has at least 99.9%, at least 99.5%, at least 99%, at least 98%,at least 97%, at least 96%, at least 95%, at least 94%, at least 93%, atleast 92%, at least 91%, at least 90%, at least 85%, at least 80%, or atleast 75% sequence identity with a polynucleotide selected from thegroup consisting of SEQ ID NOs: 24 to 46, 53 to 58, 64 to 65, 68 to 70,and fragments thereof. In another aspect, an edited nucleic acidsequence provided herein has at least 99.9%, at least 99.5%, at least99%, at least 98%, at least 97%, at least 96%, at least 95%, at least94%, at least 93%, at least 92%, at least 91%, at least 90%, at least85%, at least 80%, or at least 75% sequence identity with apolynucleotide encoding a polypeptide selected from the group consistingof SEQ ID NOs: 1 to 23, 47 to 52, 64 to 65, and 68 to 70.

Meganucleases, ZFNs, TALENs, CRISPR/Cas9, CRISPR/Csm1, CRISPR/CasX,CRISPR/CasY, and CRISPR/Cpf1 induce a double-strand DNA break at atarget site of a genomic sequence that is then repaired by the naturalprocesses of homologous recombination (HR) or non-homologous end-joining(NHEJ). Sequence modifications then occur at the cleaved sites, whichcan include deletions or insertions that result in gene disruption inthe case of NHEJ, or integration of donor nucleic acid sequences by HR.In one aspect, a method provided herein comprises editing a plant genomewith a nuclease provided herein to mutate at least 1, at least 2, atleast 3, at least 4, at least 5, at least 6, at least 7, at least 8, atleast 9, at least 10, or more than 10 nucleotides in the plant genomevia HR with a donor polynucleotide. In one aspect, a mutation providedherein is caused by genome editing using a nuclease. In another aspect,a mutation provided herein is caused by non-homologous end-joining orhomologous recombination.

In one aspect, a mutation provided herein provides a dominant mutantthat activates the expression or activity of a gene of interest, e.g., agene selected from the group consisting of a biosynthetic enzyme, aregulatory transcription factor, a transporter, a catabolic enzyme, or acombination thereof, for one or more antioxidants. Exemplary proteinsinclude, but are not limited to, AtPAP1, NtPAP1, NtMYB3-like, NtJAF13,and AtTTG1.

In one aspect, a mutation provided herein provides a dominant mutantthat activates the expression or activity of a gene of interest, e.g., agene selected from the group consisting of a biosynthetic enzyme, aregulatory transcription factor, a transporter, a catabolic enzyme, or acombination thereof, for one or more anthocyanins. Exemplary proteinsinclude, but are not limited to, AtPAP1, NtPAP1, NtMYB3-like, NtJAF13,AtTTG1, Chorismate Mutase (CM), CM-like proteins, PrephenateAminotransferase (PAT), PAT-like proteins, Arogenate Dehydratase (ADT),ADT-like proteins, Prephenate Dehydratase (PDT), PDT-like proteins,Aromatic Amino Acid Aminotransferase (AAAAT), AAAAT-like proteins,Anthocyanidin synthase2 (NtANS2), Dihyfroflavonol-4-reductase (NtDFR2),Shikimate O-hydroxycinnamoyl transferase (HCT), HCT-like proteins,Hydroxycinnamoyl CoA quinate Transferase (HQT), and HQT-like proteins.

In one aspect, a mutation provided herein provides a dominant mutantthat activates the expression or activity of a gene of interest, e.g., agene selected from the group consisting of a phenylalanine biosyntheticenzyme, a regulator of phenylalanine biosynthesis, or a phenylalaninemetabolic enzyme, or a combination thereof, for one or moreanthocyanins. Exemplary proteins include, but are not limited to,Chorismate Mutase (CM), CM-like proteins, Prephenate Aminotransferase(PAT), PAT-like proteins, Arogenate Dehydratase (ADT), ADT-likeproteins, Prephenate Dehydratase (PDT), PDT-like proteins, AromaticAmino Acid Aminotransferase (AAAAT), AAAAT-like proteins, Anthocyanidinsynthase2 (NtANS2), Dihyfroflavonol-4-reductase (NtDFR2), ShikimateO-hydroxycinnamoyl transferase (HCT), HCT-like proteins,Hydroxycinnamoyl CoA quinate Transferase (HQT), and HQT-like proteins

Meganucleases, which are commonly identified in microbes, are uniqueenzymes with high activity and long recognition sequences (>14 bp)resulting in site-specific digestion of target DNA. Engineered versionsof naturally occurring meganucleases typically have extended DNArecognition sequences (for example, 14 to 40 bp). The engineering ofmeganucleases can be more challenging than that of ZFNs and TALENsbecause the DNA recognition and cleavage functions of meganucleases areintertwined in a single domain. Specialized methods of mutagenesis andhigh-throughput screening have been used to create novel meganucleasevariants that recognize unique sequences and possess improved nucleaseactivity.

ZFNs are synthetic proteins consisting of an engineered zinc fingerDNA-binding domain fused to the cleavage domain of the FokI restrictionendonuclease. ZFNs can be designed to cleave almost any long stretch ofdouble-stranded DNA for modification of the zinc finger DNA-bindingdomain. ZFNs form dimers from monomers composed of a non-specific DNAcleavage domain of FokI endonuclease fused to a zinc finger arrayengineered to bind a target DNA sequence.

The DNA-binding domain of a ZFN is typically composed of 3-4 zinc-fingerarrays. The amino acids at positions −1, +2, +3, and +6 relative to thestart of the zinc finger cc-helix, which contribute to site-specificbinding to the target DNA, can be changed and customized to fit specifictarget sequences. The other amino acids form the consensus backbone togenerate ZFNs with different sequence specificities. Rules for selectingtarget sequences for ZFNs are known in the art.

The FokI nuclease domain requires dimerization to cleave DNA andtherefore two ZFNs with their C-terminal regions are needed to bindopposite DNA strands of the cleavage site (separated by 5-7 bp). The ZFNmonomer can cute the target site if the two-ZF-binding sites arepalindromic. The term ZFN, as used herein, is broad and includes amonomeric ZFN that can cleave double stranded DNA without assistancefrom another ZFN. The term ZFN is also used to refer to one or bothmembers of a pair of ZFNs that are engineered to work together to cleaveDNA at the same site.

Without being limited by any scientific theory, because the DNA-bindingspecificities of zinc finger domains can in principle be re-engineeredusing one of various methods, customized ZFNs can theoretically beconstructed to target nearly any gene sequence. Publicly availablemethods for engineering zinc finger domains include Context-dependentAssembly (CoDA), Oligomerized Pool Engineering (OPEN), and ModularAssembly.

TALENs are artificial restriction enzymes generated by fusing thetranscription activator-like effector (TALE) DNA binding domain to aFokI nuclease domain. When each member of a TALEN pair binds to the DNAsites flanking a target site, the FokI monomers dimerize and cause adouble-stranded DNA break at the target site. The term TALEN, as usedherein, is broad and includes a monomeric TALEN that can cleave doublestranded DNA without assistance from another TALEN. The term TALEN isalso used to refer to one or both members of a pair of TALENs that worktogether to cleave DNA at the same site.

Transcription activator-like effectors (TALEs) can be engineered to bindpractically any DNA sequence. TALE proteins are DNA-binding domainsderived from various plant bacterial pathogens of the genus Xanthomonas.The X pathogens secrete TALEs into the host plant cell during infection.The TALE moves to the nucleus, where it recognizes and binds to aspecific DNA sequence in the promoter region of a specific DNA sequencein the promoter region of a specific gene in the host genome. TALE has acentral DNA-binding domain composed of 13-28 repeat monomers of 33-34amino acids. The amino acids of each monomer are highly conserved,except for hypervariable amino acid residues at positions 12 and 13. Thetwo variable amino acids are called repeat-variable diresidues (RVDs).The amino acid pairs NI, NG, HD, and NN of RVDs preferentially recognizeadenine, thymine, cytosine, and guanine/adenine, respectively, andmodulation of RVDs can recognize consecutive DNA bases. This simplerelationship between amino acid sequence and DNA recognition has allowedfor the engineering of specific DNA binding domains by selecting acombination of repeat segments containing the appropriate RVDs.

Besides the wild-type FokI cleavage domain, variants of the FokIcleavage domain with mutations have been designed to improve cleavagespecificity and cleavage activity. The FokI domain functions as a dimer,requiring two constructs with unique DNA binding domains for sites inthe target genome with proper orientation and spacing. Both the numberof amino acid residues between the TALEN DNA binding domain and the FokIcleavage domain and the number of bases between the two individual TALENbinding sites are parameters for achieving high levels of activity.

The relationship between amino acid sequence and DNA recognition of theTALE binding domain allows for designable proteins. Software programssuch as DNA Works can be used to design TALE constructs. Other methodsof designing TALE constructs are known to those of skill in the art. SeeDoyle et al,. Nucleic Acids Research (2012) 40: W117-122.; Cermak etal., Nucleic Acids Research (2011). 39:e82; andtale-nt.cac.cornell.edu/about.

A CRISPR/Cas9 system, CRISPR/Csm1, CRISPR/CasX, CRISPR/CasY, or aCRISPR/Cpf1 system are alternatives to the FokI-based methods ZFN andTALEN. The CRISPR systems are based on RNA-guided engineered nucleasesthat use complementary base pairing to recognize DNA sequences at targetsites.

CRISPR/Cas9, CRISPR/Csm1, CRISPR/CasX, CRISPR/CasY, and a CRISPR/Cpf1systems are part of the adaptive immune system of bacteria and archaea,protecting them against invading nucleic acids such as viruses bycleaving the foreign DNA in a sequence-dependent manner. The immunity isacquired by the integration of short fragments of the invading DNA knownas spacers between two adjacent repeats at the proximal end of a CRISPRlocus. The CRISPR arrays, including the spacers, are transcribed duringsubsequent encounters with invasive DNA and are processed into smallinterfering CRISPR RNAs (crRNAs) approximately 40 nt in length, whichcombine with the trans-activating CRISPR RNA (tracrRNA) to activate andguide the Cas9 nuclease. This cleaves homologous double-stranded DNAsequences known as protospacers in the invading DNA. A prerequisite forcleavage is the presence of a conserved protospacer-adjacent motif (PAM)downstream of the target DNA, which usually has the sequence 5-NGG-3 butless frequently NAG. Specificity is provided by the so-called “seedsequence” approximately 12 bases upstream of the PAM, which must matchbetween the RNA and target DNA. Cpf1 acts in a similar manner to Cas9,but Cpf1 does not require a tracrRNA.

In still another aspect, a modified tobacco plant provided hereinfurther comprises one or more mutations in one or more loci encoding anicotine demethylase (e.g., CYP82E4, CYP82E5, CYP82E10) that conferreduced amounts of nornicotine (See U.S. Pat. Nos. 8,319,011; 8,124,851;9,187,759; 9,228,194; 9,228,195; 9,247,706) compared to control plantlacking one or more mutations in one or more loci encoding a nicotinedemethylase. In one aspect, a tobacco variety comprising mutations inthree nicotine demethylase genes is referred to as an SRC variety. Inanother aspect, an SRC variety comprises at least one mutation in eachof CYP82E4, CYP82E5, and CYP82E10. These varieties will have the lettersSRC as part of their names to differentiate from the Low Converter (LC)varieties. SRC stands for Stable Reduced Converter which identified theeffect of the technology in reducing the conversion of nicotine tonornicotine. In still another aspect, SRC varieties will furthercomprise blank shank resistance. In one aspect, a modified tobacco plantdescribed herein further comprises reduced nicotine demethylase activitycompared to a control plant when grown and cured under comparableconditions. In another aspect, a modified tobacco plant described hereinfurther comprises a reduced level of total alkaloids compared to thecontrol plant when grown and cured under comparable conditions.

In another aspect, a tobacco plant provided herein further comprises oneor more mutations in a Nic1 locus, a Nic2 locus, or both, which conferreduced amounts of nicotine compared to a control plant lacking one ormore mutations in a Nic1 locus, a Nic2 locus, or both. In anotheraspect, a modified tobacco plant described herein further comprises areduced level of nicotine compared to the control plant when grown andcured under comparable conditions. In a further aspect, a modifiedtobacco plant described herein comprises a substantially similar levelof nicotine compared to the control plant when grown and cured undercomparable conditions.

In one aspect, a modified tobacco plant described herein is a cisgenicplant. As used herein, “cisgenesis” or “cisgenic” refers to geneticmodification of a plant, plant cell, or plant genome in which allcomponents (e.g., promoter, donor nucleic acid, selection gene) haveonly plant origins (i.e., no non-plant origin components are used). Inone aspect, a modified plant, plant cell, or plant genome providedherein is cisgenic. Cisgenic plants, plant cells, and plant genomesprovided herein can lead to ready-to-use tobacco lines. In anotheraspect, a modified tobacco plant provided herein comprises nonon-tobacco genetic material or sequences. In one aspect, a cisgenicconstruct of the present disclosure encodes a polynucleotide selectedfrom the group consisting of Ubi4-P:PAP1-HSP-T (SEQ ID NO:59),Ubi4-P:NtAN2-HSP-T(SEQ ID NO:60), Tub-P:NtAN2-HSP-T(SEQ ID NO:61),Ubi4-P:NtAN2-HSP-T:Tub-P:NtAN2-HSP-T(SEQ ID NO:62), andUbi4-P:NtAN1a-HSP-T:Tub-P:NtAN2-HSP-T (SEQ ID NO:63).

In one aspect, a modified tobacco plant described herein comprises oneor more transgenes or recombinant DNA constructs capable of providing areduced level of one or more TSNAs compared to a control plant withoutthe one or more transgenes. In another aspect, a modified tobacco plantcomprises one or more transgenes or recombinant DNA constructs furtherproviding the one or more traits selected from the group consisting of:i. a reduced level of nitrite, ii. an increased level of oxygen radicleabsorbance capacity (ORAC), and iii. an increased level of one or moreantioxidants; wherein the reduced or increased level is compared to acontrol tobacco plant when grown and cured under comparable.

In another aspect, a modified tobacco plant comprises one or moretransgenes or recombinant DNA constructs encoding a biosynthetic enzyme,a regulatory transcription factor, a transporter, a catabolic enzyme, ora combination thereof, for one or more antioxidants selected from thegroup consisting of anthocyanidin, flavanone, flavanol, flavone,flavonol, isoflavone, hydroxybenzoic acid, hydroxycinnamic acid,ellagitannin, stibene, lignan, carotenoids, and glycyrrhzin. In anotheraspect, a modified tobacco plant comprises one or more transgenes orrecombinant DNA constructs encoding a biosynthetic enzyme, a regulatorytranscription factor, a transporter, a catabolic enzyme, or acombination thereof, for one or more antioxidants selected from thegroup consisting of Delphnidin, Cyanidin, Procyanidin, Prodelphinidin,Hesperetin, Perlargonidin, Peonidin, Petunidin, Naringenin, Catechin,Epicatechin, Apigenin, Luteonin, Quercetin, Myricetin, Rutin, Genistein,Daidzein, Gallic acid, Vanillic acid, Protocatechuic acid, Ferunic acid,Cinnamic acid, Coumeric acid, Chlorogenic acid, Coffeic acid, ferulicacid, Sanguiin, Resveratrol, Sesamin, Caretonoids, and Vitamin C. Inanother aspect, a modified tobacco plant comprises one or moretransgenes or recombinant DNA constructs encoding phenylalaninebiosynthetic enzymes, regulators of phenylalanine biosynthesis, orphenylalanine metabolic enzymes, or a combination thereof. In oneaspect, one or more transgenes or recombinant DNA constructs encode apolypeptide having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, 99%, or 100% identity to a sequence selected from thegroup consisting of SEQ ID Nos: 1 to 23, 47 to 52, 64 to 65, and 68 to70. In another aspect, one or more transgenes or recombinant DNAconstructs encode a gene comprise a coding sequence having at least 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%identity to a sequence selected from the group consisting of SEQ ID Nos:24 to 46, 53 to 58, 66 to 67, and 71 to 73.

In one aspect, a recombinant DNA construct of the present disclosurecomprises a promoter capable of driving gene transcription in a plant,operably linked to a polynucleotide encoding a polypeptide having atleast 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99% or100% sequence identity to a polypeptide selected from the groupconsisting of SEQ ID NOs: 1 to 23, 47 to 52, 64 to 65, and 68 to 70. Inone aspect, a recombinant DNA construct or expression cassette in atransgene provided herein comprises a promoter selected from the groupconsisting of a constitutive promoter, an inducible promoter, and atissue-preferred promoter (for example, without being limiting, aleaf-specific promoter, a shoot-specific promoter, a root-specificpromoter, or a meristem-specific promoter).

Exemplary constitutive promoters include the core promoter of the Rsyn7promoter and other constitutive promoters disclosed in U.S. Pat. No.6,072,050; the core CaMV 35S promoter (Odell et al. (1985) Nature313:810-812); ubiquitin (Christensen et al. (1989) Plant Mol. Biol.12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689);pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten etal. (1984) EMBO J 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026),and the like.

Exemplary chemical-inducible promoters include the tobacco PR-1apromoter, which is activated by salicylic acid. Other chemical-induciblepromoters of interest include steroid-responsive promoters (see, forexample, the glucocorticoid-inducible promoter in Schena et al. (1991)Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998)Plant J. 14(2):247-257) and tetracycline-inducible promoters (see, forexample, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat.Nos. 5,814,618 and 5,789,156). Additional exemplary promoters that canbe used herein are those responsible for heat-regulated gene expression,light-regulated gene expression (for example, the pea rbcS-3A; the maizerbcS promoter; the chlorophyll alb-binding protein gene found in pea; orthe Arabssu promoter), hormone-regulated gene expression (for example,the abscisic acid (ABA) responsive sequences from the Em gene of wheat;the ABA-inducible HVA1 and HVA22, and rd29A promoters of barley andArabidopsis; and wound-induced gene expression (for example, of wunl),organ specific gene expression (for example, of the tuber-specificstorage protein gene; the 23-kDa zein gene from maize described by; orthe French bean (β-phaseolin gene), or pathogen-inducible promoters (forexample, the PR-1, prp-1, or (13-1,3 glucanase promoters, thefungal-inducible wirla promoter of wheat, and the nematode-induciblepromoters, TobRB7-5A and Hmg-1, of tobacco arid parsley, respectively).

Additional exemplary tissue-preferred promoters include those disclosedin Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997)Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen. Genet.254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168;Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al.(1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) PlantPhysiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol.35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20:181-196; Orozcoet al. (1993) Plant Mol. Biol. 23(6):1129-1138; Matsuoka et al. (1993)Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia et al.(1993) Plant J. 4(3):495-505.

As used herein, “operably linked” refers to a functional linkage betweentwo or more elements. For example, an operable linkage between apolynucleotide of interest and a regulatory sequence (e.g., a promoter)is a functional link that allows for expression of the polynucleotide ofinterest. Operably linked elements may be contiguous or non-contiguous.

In one aspect, a transgene provided herein comprises a heterologous ornon-tobacco promoter or coding sequence. In another aspect, a transgeneprovided herein comprises a endogenous or tobacco-origin promoter orcoding sequence. As used herein, “heterologous” refers to a sequencethat originates from a foreign species, or, if from the same species, issubstantially modified from its native form in composition and/orgenomic locus by deliberate human intervention. The term also isapplicable to nucleic acid constructs, also referred to herein as“polynucleotide constructs” or “nucleotide constructs.” In this manner,a “heterologous” nucleic acid construct is intended to mean a constructthat originates from a foreign species, or, if from the same species, issubstantially modified from its native form in composition and/orgenomic locus by deliberate human intervention. Heterologous nucleicacid constructs include, but are not limited to, recombinant nucleotideconstructs that have been introduced into a plant or plant part thereof,for example, via transformation methods or subsequent breeding of atransgenic plant with another plant of interest.

In one aspect, a recombinant DNA construct, modified plant, seed, plantcomponent, plant cell, or plant genome provided herein comprises aheterologous promoter operably linked to a polynucleotide encoding apolypeptide having at least 40%, at least 50%, at least 60%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, at least 99%, or 100% sequence identityto a polypeptide selected from the group consisting of SEQ ID NOs: 24 to46, 53 to 58, 66 to 67, and 71 to 73.

Enhancer elements are regions of DNA that can be bound by proteins toactivate RNA transcription. In one aspect, a promoter sequence usedherein is operably linked to an enhancer element. In one aspect, anenhancer element provided herein is a CsVMV promoter.

Also provided herein are the transformation of tobacco plants withrecombinant constructs or expression cassettes described herein usingany suitable transformation methods known in the art. Methods forintroducing polynucleotide sequences into tobacco plants are known inthe art and include, but are not limited to, stable transformationmethods, transient transformation methods, and virus-mediated methods.“Stable transformation” refers to transformation where the nucleotideconstruct of interest introduced into a plant integrates into a genomeof the plant and is capable of being inherited by the progeny thereof.“Transient transformation” is intended to mean that a sequence isintroduced into the plant and is only temporally expressed or is onlytransiently present in the plant.

In one aspect, methods and compositions provided herein comprise theintroduction of one or more polynucleotides into one or more plantcells. In one aspect, a plant genome provided herein is modified toinclude an introduced polynucleotide or recombinant DNA construct. Asused herein, “plant genome” refers to a nuclear genome, a mitochondrialgenome, or a plastid (e.g., chloroplast) genome of a plant cell. Inanother aspect, a polynucleotide provided herein is integrated into anartificial chromosome. In one aspect, an artificial chromosomecomprising a polynucleotide provided herein is integrated into a plantcell.

In one aspect, transgenes provided herein comprise a recombinant DNAconstruct. In one aspect, recombinant DNA constructs or expressioncassettes provided herein can comprise a selectable marker gene for theselection of transgenic cells. Selectable marker genes include, but arenot limited to, genes encoding antibiotic resistance, such as thoseencoding neomycin phosphotransferase II (NEO) and hygromycinphosphotransferase (HPT), as well as genes conferring resistance toherbicidal compounds, such as glufosinate ammonium, bromoxynil,imidazolinones, triazolopyrimidines, sulfonylurea (e.g., chlorsulfuronand sulfometuron methyl), and 2,4-dichlorophenoxyacetate (2,4-D).Additional selectable markers include phenotypic markers such asβ-galactosidase and fluorescent proteins such as green fluorescentprotein (GFP).

In one aspect, methods and compositions provided herein comprise avector. As used herein, the terms “vector” or “plasmid” are usedinterchangeably and refer to a circular, double-stranded DNA moleculethat is physically separate from chromosomal DNA. In one aspect, aplasmid or vector used herein is capable of replication in vivo. A“transformation vector,” as used herein, is a plasmid that is capable oftransforming a plant cell. In an aspect, a plasmid provided herein is abacterial plasmid. In another aspect, a plasmid provided herein is anAgrobacterium Ti plasmid or derived from an Agrobacterium Ti plasmid.

In one aspect, a plasmid or vector provided herein is a recombinantvector. As used herein, the term “recombinant vector” refers to a vectorformed by laboratory methods of genetic recombination, such as molecularcloning. In another aspect, a plasmid provided herein is a syntheticplasmid. As used herein, a “synthetic plasmid” is an artificiallycreated plasmid that is capable of the same functions (e.g.,replication) as a natural plasmid (e.g., Ti plasmid). Without beinglimited, one skilled in the art can create a synthetic plasmid de novovia synthesizing a plasmid by individual nucleotides, or by splicingtogether nucleic acid molecules from different pre-existing plasmids.

Vectors are commercially available or can be produced by recombinant DNAtechniques routine in the art. A vector containing a nucleic acid canhave expression elements operably linked to such a nucleic acid, andfurther can include sequences such as those encoding a selectable marker(e.g., an antibiotic resistance gene). A vector containing a nucleicacid can encode a chimeric or fusion polypeptide (i.e., a polypeptideoperatively linked to a heterologous polypeptide, which can be at eitherthe N-terminus or C-terminus of the polypeptide). Representativeheterologous polypeptides are those that can be used in purification ofthe encoded polypeptide (e.g., 6xHis tag, glutathione S-transferase(GST)).

Suitable methods of introducing polynucleotides (e.g., transgenes,recombinant vectors, recombinant DNA constructs, expression constructs)into plant cells of the present disclosure include microinjection(Crossway et al. (1986) Biotechniques 4:320-334), electroporation(Shillito et al. (1987) Meth. Enzymol. 153:313-336; Riggs et al. (1986)Proc. Natl. Acad. Sci. USA 83:5602-5606), Agrobacterium-mediatedtransformation (U.S. Pat. Nos. 5,104,310, 5,149,645, 5,177,010,5,231,019, 5,463,174, 5,464,763, 5,469,976, 4,762,785, 5,004,863,5,159,135, 5,563,055, and 5,981,840), direct gene transfer (Paszkowskiet al. (1984) EMBO 1 3:2717-2722), and ballistic particle acceleration(see, for example, U.S. Pat. Nos. 4,945,050, 5,141,131, 5,886,244,5,879,918, and 5,932,782; Tomes et al. (1995) in Plant Cell, Tissue, andOrgan Culture Fundamental Methods, ed. Gamborg and Phillips(Springer-Verlag, Berlin); McCabe et al. (1988) Biotechnology6:923-926). Also see Weissinger et al. (1988) Ann. Rev. Genet.22:421-477; Christou et al. (1988) Plant Physiol. 87:671-674 (soybean);McCabe et al. (1988) Bio/Technology 6:923-926 (soybean); Finer andMcMullen (1991) In Vitro Cell Dev. Biol. 27P: 175-182 (soybean); Singhet al. (1998) Theor. Appl. Genet. 96:319-324 (soybean); De Wet et al.(1985) in The Experimental Manipulation of Ovule Tissues, ed. Chapman etal. (Longman, N.Y.), pp. 197-209 (pollen); Kaeppler et al. (1990) PlantCell Reports 9:415-418 and Kaeppler et al. (1992) Theor. Appl. Genet.84:560-566 (whisker-mediated transformation); D'Halluin et al. (1992)Plant Cell 4:1495-1505 (electroporation). In one aspect, a bacterialcell provided herein comprises a recombinant DNA construct orrecombinant vector provided herein.

In another aspect, recombinant constructs or expression cassettesprovided herein may be introduced into plants by contacting plants witha virus or viral nucleic acids. Generally, such methods involveincorporating an expression cassette of the present disclosure within aviral DNA or RNA molecule. It is recognized that promoters for use inthe expression cassettes provided herein also encompass promotersutilized for transcription by viral RNA polymerases. Methods forintroducing polynucleotides into plants and expressing a protein encodedtherein, involving viral DNA or RNA molecules, are known in the art.See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785,5,589,367, 5,316,931, and Porta et al. (1996) Molecular Biotechnology5:209-221.

Any plant tissue that can be subsequently propagated using clonalmethods, whether by organogenesis or embryogenesis, may be transformedwith a recombinant construct or an expression cassette provided herein.By “organogenesis” in intended the process by which shoots and roots aredeveloped sequentially from meristematic centers. By “embryogenesis” isintended the process by which shoots and roots develop together in aconcerted fashion (not sequentially), whether from somatic cells orgametes. Exemplary tissues that are suitable for various transformationprotocols described herein include, but are not limited to, callustissue, existing meristematic tissue (e.g., apical meristems, axillarybuds, and root meristems) and induced meristem tissue (e.g., cotyledonmeristem and hypocotyl meristem), hypocotyls, cotyledons, leaf disks,pollen, embryos, and the like.

It is understood that any modified tobacco plant of the presentdisclosure can further comprise additional agronomically desirabletraits, for example, by transformation with a genetic construct ortransgene using a technique known in the art. Without limitation, anexample of a desired trait is herbicide resistance, pest resistance,disease resistance, high yield, high grade index value, curability,curing quality, mechanical harvestability, holding ability, leafquality, height, plant maturation (e.g., early maturing, early to mediummaturing, medium maturing, medium to late maturing, or late maturing),stalk size (e.g., a small, medium, or a large stalk), or leaf number perplant (e.g., a small (e.g., 5-10 leaves), medium (e.g., 11-15 leaves),or large (e.g., 16-21) number of leaves), or any combination. In oneaspect, tobacco plants capable of producing cured leaf with reduced TSNAor seeds provided herein comprise one or more transgenes expressing oneor more insecticidal proteins, such as, for example, a crystal proteinof Bacillus thuringiensis or a vegetative insecticidal protein fromBacillus cereus, such as VIP3 (see, for example, Estruch et al.(1997)Nat. Biotechnol.15:137). In another aspect, tobacco plantsprovided herein further comprise an introgressed trait conferringresistance to brown stem rot (U.S. Pat. No. 5,689,035) or resistance tocyst nematodes (U.S. Pat. No. 5,491,081).

The level and/or activity of polypeptides provided herein may bemodulated by employing a polynucleotide that is not capable ofdirecting, in a transformed plant, the expression of a protein or anRNA. For example, the polynucleotides of the invention may be used todesign polynucleotide constructs that can be employed in methods foraltering or mutating a genomic nucleotide sequence in an organism. Suchpolynucleotide constructs include, but are not limited to, RNA:DNAvectors, RNA:DNA mutational vectors, RNA:DNA repair vectors,mixed-duplex oligonucleotides, self-complementary RNA:DNAoligonucleotides and recombinogenic oligonucleobases. Such nucleotideconstructs and methods of use are known in the art. See, U.S. Pat. Nos.5,565,350; 5,731,181; 5,756,325; 5,760,012; 5,795,972 and 5,871,984;each of which is incorporated herein by reference as if set forth in itsentirety. See also, International Patent Application Publication Nos. WO98/149350, WO 99/107865 and WO 99/125921; and Beetham et al. (1999)Proc. Natl. Acad. Sci. USA 96:8774-8778; each of which is incorporatedherein by reference as if set forth in its entirety.

The present disclosure also provides compositions and methods forinhibiting the expression or function of one or more polypeptides thatsuppress, directly or indirectly, the production or accumulation of oneor more antioxidants in a plant, particularly plants of the Nicotianatabacum genus, including tobacco plants of various commercial varieties.

In one aspect, inhibition of the expression of one or more polypeptidesprovided herein may be obtained by RNA interference (RNAi) by expressionof a transgene capable of producing an inhibitory sequence providedherein. In one aspect, RNAi comprises expressing a non-coding RNA. Asused herein, a “non-coding RNA” is selected from the group consisting ofa microRNA (miRNA), a small interfering RNA (siRNA), a trans-actingsiRNA (ta-siRNA), a transfer RNA (tRNA), a ribosomal RNA (rRNA), anintron, a hairpin RNA (hpRNA), and an intron-containing hairpin RNA(ihpRNA). In one aspect, a single non-coding RNA provided hereininhibits the expression of at least 1, at least 2, at least 3, at least4, at least 5, at least 6, at least 7, at least 8, at least 9, at least10, or more than 10 polypeptides. In one aspect, a non-coding RNAprovided herein is stably transformed into a plant genome. In anotheraspect, a non-coding RNA provided herein is transiently transformed intoa plant genome.

As used herein, the terms “suppress,” “inhibit,” “inhibition,”“inhibiting”, and “downregulation” are defined as any method known inthe art or described herein that decreases the expression or function ofa gene product (e.g., an mRNA, a protein, a non-coding RNA).“Inhibition” can be in the context of a comparison between two cells,for example, a modified cell versus a control cell. Inhibition ofexpression or function of a gene product can also be in the context of acomparison between plant cells, organelles, organs, tissues, or plantcomponents within the same plant or between different plants, andincludes comparisons between developmental or temporal stages within thesame plant or plant component or between plants or plant components.“Inhibition” includes any relative decrement of function or productionof a gene product of interest, up to and including complete eliminationof function or production of that gene product. The term “inhibition”encompasses any method or composition that down-regulates translationand/or transcription of the target gene product or functional activityof the target gene product. “Inhibition” need not comprise completeelimination of expression of a gene product. In an aspect, a geneproduct in a modified cell provided herein comprises expression that isat least 1%, at least 2%, at least 3%, at least 4%, at least 5%, atleast 10%, at least 20%, at least 25%, at least 30%, at least 40%, atleast 50%, at least 60%, at least 70%, at least 80%, at least 90%, atleast 95%, or 100% lower than the expression of the gene product in acontrol cell. In another aspect, a gene product in a modified cellprovided herein comprises expression that is between 1% and 100%,between 1% and 95%, between 1% and 90%, between 1% and 80%, between 1%and 70%, between 1% and 60%, between 1% and 50%, between 1% and 40%,between 1% and 30%, between 1% and 25%, between 1% and 20%, between 1%and 15%, between 1% and 10%, between 1% and 5%, between 5% and 25%,between 5% and 50%, between 5% and 75%, between 5% and 100%, between 10%and 25%, between 10% and 50%, between 10% and 75%, between 10% and 100%,between 25% and 50%, between 25% and 75%, between 25% and 100%, orbetween 50% and 100% lower than the expression of the gene product in acontrol cell.

As used herein, a “target site” refers to a location of a polynucleotidesequence that is bound to and cleaved by a site-specific nucleaseintroducing a double stranded break into the nucleic acid backbone. Inanother aspect a target site comprises at least 10, at least 11, atleast 12, at least 13, at least 14, at least 15, at least 16, at least17, at least 18, at least 19, at least 20, at least 21, at least 22, atleast 23, at least 24, at least 25, at least 26, at least 27, at least29, or at least 30 consecutive nucleotides. In another aspect, a targetsite provided herein is at least 10, at least 20, at least 30, at least40, at least 50, at least 75, at least 100, at least 125, at least 150,at least 200, at least 250, at least 300, at least 400, or at least 500nucleotides. In one aspect a site-specific nuclease binds to a targetsite. In another aspect a site-specific nuclease binds to a target sitevia a guiding non-coding RNA (i.e., such as, without being limiting, aCRISPR RNA or single-guide RNA (both described in detail below)). In oneaspect, a non-coding RNA provided herein is complementary to a targetsite. It will be appreciated that perfect complementarity is notrequired for a non-coding RNA to bind to a target site; at least 1, atleast 2, at least 3, at least 4, or at least 5, at least 6, at least 7or at least 8 mismatches between a target site and a non-coding RNA canbe tolerated. As used herein, a “target region” or a “targeted region”refers to a polynucleotide sequence that is desired to be modified. Inone aspect, a “target region,” “targeted region,” or a “target gene” isflanked by two or more, three or more, four or more, five or more, sixor more, seven or more, eight or more, nine or more, or ten or moretarget sites. A “target gene” refers to a polynucleotide sequenceencoding a gene that is desired to be modified or from which transcriptexpression is desired to be modulated. In one aspect, a polynucleotidesequence comprising a target gene further comprises one or more targetsites. In another aspect, a transgene is said to be targeting a targetsite or a target gene. In another aspect, a target region comprises oneor more, two or more, three or more, four or more, five or more, six ormore, seven or more, eight or more, nine or more, or ten or more targetgenes. Without being limiting, in one aspect a target region can besubject to deletion or inversion. As used herein, “flanked” when used todescribe a target region, refers to two or more target sites physicallysurrounding the target region, with one target site on each side of thetarget region.

As used herein, in the context of a transgene “directly modulating” or“directly modulates” refers to inducing a change in the transcript orprotein level of a target gene by an agent produced by the transgene andsharing sufficient homology with at least a portion of the target gene.Direct modulation can result in a change in transcriptional activity,transcript stability, transcript constitution, or transcript expressionlevel which can either increase or decrease the number of transcriptsavailable for translation and can either increase or decrease the numberof protein molecules.

A target site can be positioned in a polynucleotide sequence encoding aleader, an enhancer, a transcriptional start site, a promoter, a 5′-UTR,an exon, an intron, a 3′-UTR, a polyadenylation site, or a terminationsequence. It will be appreciated that a target site can be also bepositioned upstream or downstream of a sequence encoding a leader, anenhancer, a transcriptional start site, a promoter, a 5′-UTR, an exon,an intron, a 3′-UTR, a polyadenylation site, or a termination sequence.In one aspect, a target site is positioned within 10, within 20, within30, within 40, within 50, within 75, within 100, within 125, within 150,within 200, within 250, within 300, within 400, within 500, within 600,within 700, within 800, within 900, within 1000, within 1250, within1500, within 2000, within 2500, within 5000, within 10,000, or within25,000 nucleotides of a polynucleotide encoding a leader, an enhancer, atranscriptional start site, a promoter, a 5′-UTR, an exon, an intron, a3′-UTR, a polyadenylation site, a gene, or a termination sequence.

As used herein, “upstream” refers to a nucleic acid sequence that ispositioned before the 5′ end of a linked nucleic acid sequence. As usedherein, “downstream” refers to a nucleic acid sequence is positionedafter the 3′ end of a linked nucleic acid sequence. As used herein, “5”′refers to the start of a coding DNA sequence or the beginning of an RNAmolecule. As used herein, “3′” refers to the end of a coding DNAsequence or the end of an RNA molecule. It will be appreciated that an“inversion” refers to reversing the orientation of a givenpolynucleotide sequence. For example, if the sample sequence5′-ATGATC-3′ is inverted it will read 5′-CTAGTA-3′ in reverseorientation. Additionally, the sample sequence 5′-ATGATC-3′ isconsidered to be in “opposite orientation” to the sample sequence5′-CTAGTA-3′.

The term “inhibitory sequence” encompasses any polynucleotide orpolypeptide sequence capable of inhibiting the expression or function ofa gene in a plant, such as full-length polynucleotide or polypeptidesequences, truncated polynucleotide or polypeptide sequences, fragmentsof polynucleotide or polypeptide sequences, variants of polynucleotideor polypeptide sequences, sense-oriented nucleotide sequences,antisense-oriented nucleotide sequences, the complement of a sense- orantisense-oriented nucleotide sequence, inverted regions of nucleotidesequences, hairpins of nucleotide sequences, double-stranded nucleotidesequences, single-stranded nucleotide sequences, combinations thereof,and the like. The term “polynucleotide sequence” includes sequences ofRNA, DNA, chemically modified nucleic acids, nucleic acid analogs,combinations thereof, and the like.

Inhibitory sequences are designated herein by the name of the targetgene product. Thus, as a non-limiting example, an “gene X inhibitorysequence” refers to an inhibitory sequence that is capable of inhibitingthe expression of a gene X locus in a plant, for example, at the levelof transcription and/or translation, or which is capable of inhibitingthe function of a gene product. When the phrase “capable of inhibiting”is used in the context of a transgene containing polynucleotideinhibitory sequence, it is intended to mean that the inhibitory sequenceitself exerts the inhibitory effect; or, where the inhibitory sequenceencodes an inhibitory nucleotide molecule (for example, hairpin RNA,miRNA, or double-stranded RNA polynucleotides), or encodes an inhibitorypolypeptide (e.g., a polypeptide that inhibits expression or function ofthe target gene product), following its transcription (for example, inthe case of an inhibitory sequence encoding a hairpin RNA, miRNA, ordouble-stranded RNA polynucleotide) or its transcription and translation(in the case of an inhibitory sequence encoding an inhibitorypolypeptide), the transcribed or translated product, respectively,exerts the inhibitory effect on the target gene product (e.g., inhibitsexpression or function of the target gene product).

An inhibitory sequence provided herein can be a sequence triggering genesilencing via any silencing pathway or mechanism known in the art,including, but not limited to, sense suppression/co-suppression, antisense suppression, double-stranded RNA (dsRNA) interference, hairpin RNAinterference and intron-containing hairpin RNA interference,amplicon-mediated interference, ribozymes, small interfering RNA,artificial or synthetic microRNA, and artificial trans-acting siRNA.

One aspect of the present application relates to methods of screeningand selecting cells for targeted edits and methods of selecting cellscomprising targeted edits. Nucleic acids can be isolated using varioustechniques. For example, nucleic acids can be isolated using any methodincluding, without limitation, recombinant nucleic acid technology,and/or the polymerase chain reaction (PCR). General PCR techniques aredescribed, for example in PCR Primer: A Laboratory Manual, Dieffenbach &Dveksler, Eds., Cold Spring Harbor Laboratory Press, 1995. Recombinantnucleic acid techniques include, for example, restriction enzymedigestion and ligation, which can be used to isolate a nucleic acid.Isolated nucleic acids also can be chemically synthesized, either as asingle nucleic acid molecule or as a series of oligonucleotides.Polypeptides can be purified from natural sources (e.g., a biologicalsample) by known methods such as DEAE ion exchange, gel filtration, andhydroxyapatite chromatography. A polypeptide also can be purified, forexample, by expressing a nucleic acid in an expression vector. Inaddition, a purified polypeptide can be obtained by chemical synthesis.The extent of purity of a polypeptide can be measured using anyappropriate method, e.g., column chromatography, polyacrylamide gelelectrophoresis, or HPLC analysis.

Also provided herein is cured tobacco material made from tobacco leaf,tobacco plants, or plant components provided herein. “Curing” is apost-harvest process that reduces moisture and brings about thedestruction of chlorophyll giving tobacco leaf a golden color and bywhich starch is converted to sugar. Cured tobacco therefore has a higherreducing sugar content and a lower starch content compared to harvestedgreen leaf. In one aspect, tobacco plants or plant components providedherein can be cured using conventional means, e.g., flue-cured,barn-cured, fire-cured, air-cured or sun-cured. See, for example, Tso(1999, Chapter 1 in Tobacco, Production, Chemistry and Technology, Davis& Nielsen, eds., Blackwell Publishing, Oxford) for a description ofdifferent types of curing methods. Cured tobacco is usually aged in awooden drum (e.g., a hogshead) or cardboard cartons in compressedconditions for several years (e.g., two to five years), at a moisturecontent ranging from 10% to about 25%. See, U.S. Pat. Nos. 4,516,590 and5,372,149. Cured and aged tobacco then can be further processed. Furtherprocessing includes conditioning the tobacco under vacuum with orwithout the introduction of steam at various temperatures,pasteurization, and fermentation. Fermentation typically ischaracterized by high initial moisture content, heat generation, and a10 to 20% loss of dry weight. See, for example, U.S. Pat. Nos.4,528,993, 4,660,577, 4,848,373, 5,372,149; U.S. Publication No.2005/0178398; and Tso (1999, Chapter 1 in Tobacco, Production, Chemistryand Technology, Davis & Nielsen, eds., Blackwell Publishing, Oxford).Cured, aged, and fermented tobacco can be further processed (e.g., cut,shredded, expanded, or blended). See, for example, U.S. Pat. Nos.4,528,993; 4,660,577; and 4,987,907. In one aspect, the cured tobaccomaterial of the present disclosure is flue-cured, sun-cured, air-cured,or fire-cured.

Tobacco material obtained from modified tobacco lines, varieties orhybrids of the present disclosure can be used to make tobacco products.As used herein, “tobacco product” is defined as any product made orderived from tobacco that is intended for human use or consumption. Inan aspect, a tobacco product provided herein comprises cured componentsfrom a modified tobacco plant provided herein. In another aspect, atobacco product provided herein comprises cured tobacco leaf from amodified tobacco plant provided herein.

Tobacco products provided herein include, without limitation, cigaretteproducts (e.g., cigarettes, bidi cigarettes, kreteks), cigar products(e.g., cigars, cigar wrapping tobacco, cigarillos), pipe tobaccoproducts, products derived from tobacco, tobacco-derived nicotineproducts, smokeless tobacco products (e.g., moist snuff, dry snuff,snus, chewing tobacco, moist smokeless tobacco, fine cut chewingtobacco, long cut chewing tobacco, pouched chewing tobacco), films,chewables (e.g., gum), lozenges, dissolving strips, tabs, tablets,shaped parts, gels, consumable units, insoluble matrices, hollow shapes,reconstituted tobacco, expanded tobacco, and the like. See, for example,U.S. Patent Publication No. US 2006/0191548.

As used herein, “cigarette” refers a tobacco product having a “rod” and“filler”. The cigarette “rod” includes the cigarette paper, filter, plugwrap (used to contain filtration materials), tipping paper that holdsthe cigarette paper (including the filler) to the filter, and all gluesthat hold these components together. The “filler” includes (1) alltobaccos, including but not limited to reconstituted and expandedtobacco, (2) non-tobacco substitutes (including but not limited toherbs, non-tobacco plant materials and other spices that may accompanytobaccos rolled within the cigarette paper), (3) casings, (4)flavorings, and (5) all other additives (that are mixed into tobaccosand substitutes and rolled into the cigarette).

In one aspect, this disclosure provides nicotine derived from and amethod of producing nicotine from a modified tobacco plant providedherein for use in a product.

In one aspect, a method provided herein comprises preparing a tobaccoproduct using cured tobacco leaf from a modified tobacco plant providedherein.

As used herein, “reconstituted tobacco” refers to a part of tobaccofiller made from tobacco dust and other tobacco scrap material,processed into sheet form and cut into strips to resemble tobacco. Inaddition to the cost savings, reconstituted tobacco is very importantfor its contribution to cigarette taste from processing flavordevelopment using reactions between ammonia and sugars.

As used herein, “expanded tobacco” refers to a part of tobacco fillerwhich is processed through expansion of suitable gases so that thetobacco is “puffed” resulting in reduced density and greater fillingcapacity. It reduces the weight of tobacco used in cigarettes.

Tobacco products derived from plants of the present disclosure alsoinclude cigarettes and other smoking articles, particularly thosesmoking articles including filter elements, where the rod of smokablematerial includes cured tobacco within a tobacco blend. In an aspect, atobacco product of the present disclosure is selected from the groupconsisting of a cigarillo, a non-ventilated recess filter cigarette, avented recess filter cigarette, a bidi cigarette, a cigar, snuff, pipetobacco, cigar tobacco, cigarette tobacco, chewing tobacco, leaftobacco, hookah tobacco, shredded tobacco, and cut tobacco. In anotheraspect, a tobacco product of the present disclosure is a smokelesstobacco product. Smokeless tobacco products are not combusted andinclude, but not limited to, chewing tobacco, moist smokeless tobacco,snus, and dry snuff. Chewing tobacco is coarsely divided tobacco leafthat is typically packaged in a large pouch-like package and used in aplug or twist. Moist smokeless tobacco is a moist, more finely dividedtobacco that is provided in loose form or in pouch form and is typicallypackaged in round cans and used as a pinch or in a pouch placed betweenan adult tobacco consumer's cheek and gum. Snus is a heat treatedsmokeless tobacco. Dry snuff is finely ground tobacco that is placed inthe mouth or used nasally. In a further aspect, a tobacco product of thepresent disclosure is selected from the group consisting of loose leafchewing tobacco, plug chewing tobacco, moist snuff, and nasal snuff. Inyet another aspect, a tobacco product of the present disclosure isselected from the group consisting of an electronically heatedcigarette, an e-cigarette, an electronic vaporing device.

The present disclosure further provides a method for manufacturing atobacco product comprising tobacco material from tobacco plants providedherein. In one aspect, methods provided herein comprise conditioningaged tobacco material made from tobacco plants provided herein toincrease its moisture content from between about 12.5% and about 13.5%to about 21%, blending the conditioned tobacco material to produce adesirable blend. In one aspect, the method of manufacturing a tobaccoproduct provided herein further comprises casing or flavoring the blend.Generally, during the casing process, casing or sauce materials areadded to blends to enhance their quality by balancing the chemicalcomposition and to develop certain desired flavor characteristics.Further details for the casing process can be found in TobaccoProduction, Chemistry and Technology, Edited by L. Davis and M. Nielsen,Blackwell Science, 1999.

Tobacco material provided herein can be also processed using methodsincluding, but not limited to, heat treatment (e.g., cooking, toasting),flavoring, enzyme treatment, expansion and/or curing. Both fermented andnon-fermented tobaccos can be processed using these techniques. Examplesof suitable processed tobaccos include dark air-cured, dark fire cured,burley, flue cured, and cigar filler or wrapper, as well as the productsfrom the whole leaf stemming operation. In one aspect, tobacco fibersinclude up to 70% dark tobacco on a fresh weight basis. For example,tobacco can be conditioned by heating, sweating and/or pasteurizingsteps as described in U.S. Publication Nos. 2004/0118422 or2005/0178398.

Tobacco material provided herein can be subject to fermentation.Fermenting typically is characterized by high initial moisture content,heat generation, and a 10 to 20% loss of dry weight. See, e.g., U.S.Pat. Nos. 4,528,993; 4,660,577; 4,848,373; and 5,372,149. In addition tomodifying the aroma of the leaf, fermentation can change either or boththe color and texture of a leaf. Also during the fermentation process,evolution gases can be produced, oxygen can be taken up, the pH canchange, and the amount of water retained can change. See, for example,U.S. Publication No. 2005/0178398 and Tso (1999, Chapter 1 in Tobacco,Production, Chemistry and Technology, Davis & Nielsen, eds., BlackwellPublishing, Oxford). Cured, or cured and fermented tobacco can befurther processed (e.g., cut, expanded, blended, milled or comminuted)prior to incorporation into the oral product. The tobacco, in somecases, is long cut fermented cured moist tobacco having an ovenvolatiles content of between 48 and 50 weight percent prior to mixingwith a copolymer and, optionally, flavorants and other additives.

In one aspect, tobacco material provided herein can be processed to adesired size. In certain aspects, tobacco fibers can be processed tohave an average fiber size of less than 200 micrometers. In one aspect,tobacco fibers are between 75 and 125 micrometers. In another aspect,tobacco fibers are processed to have a size of 75 micrometers or less.In one aspect, tobacco fibers include long cut tobacco, which can be cutor shredded into widths of about 10 cuts/inch up to about 110 cuts/inchand lengths of about 0.1 inches up to about 1 inch. Double cut tobaccofibers can have a range of particle sizes such that about 70% of thedouble cut tobacco fibers falls between the mesh sizes of −20 mesh and80 mesh.

Tobacco material provided herein can be processed to have a total ovenvolatiles content of about 10% by weight or greater; about 20% by weightor greater; about 40% by weight or greater; about 15% by weight to about25% by weight; about 20% by weight to about 30% by weight; about 30% byweight to about 50% by weight; about 45% by weight to about 65% byweight; or about 50% by weight to about 60% by weight. Those of skill inthe art will appreciate that “moist” tobacco typically refers to tobaccothat has an oven volatiles content of between about 40% by weight andabout 60% by weight (e.g., about 45% by weight to about 55% by weight,or about 50% by weight). As used herein, “oven volatiles” are determinedby calculating the percentage of weight loss for a sample after dryingthe sample in a pre-warmed forced draft oven at 110° C. for 3.25 hours.An oral product can have a different overall oven volatiles content thanthe oven volatiles content of the tobacco fibers used to make the oralproduct. The processing steps described herein can reduce or increasethe oven volatiles content.

In one aspect, tobacco plants, seeds, plant components, plant cells, andplant genomes provided herein are from a tobacco type selected from thegroup consisting of flue-cured tobacco, sun-cured tobacco, air-curedtobacco, dark air-cured tobacco, and dark fire-cured tobacco. In anotheraspect, tobacco plants, seeds, plant components, plant cells, and plantgenomes provided herein are from a tobacco type selected from the groupconsisting of Burley tobacco, Maryland tobacco, bright tobacco, Virginiatobacco, Oriental tobacco, Turkish tobacco, dark tobacco, and Galpãotobacco. In one aspect, a tobacco plant or seed provided herein is ahybrid plant or seed. As used herein, a “hybrid” is created by crossingtwo plants from different varieties or species, such that the progenycomprises genetic material from each parent. Skilled artisans recognizethat higher order hybrids can be generated as well. For example, a firsthybrid can be made by crossing Variety C with Variety D to create a C×Dhybrid, and a second hybrid can be made by crossing Variety E withVariety F to create an E×F hybrid. The first and second hybrids can befurther crossed to create the higher order hybrid (C×D)×(E×F) comprisinggenetic information from all four parent varieties.

Flue-cured tobaccos (also called Virginia or bright tobaccos) amount toapproximately 40% of world tobacco production. Flue-cured tobaccos areoften also referred to as “bright tobacco” because of the golden-yellowto deep-orange color it reaches during curing. Flue-cured tobaccos havea light, bright aroma and taste. Flue-cured tobaccos are generally highin sugar and low in oils. Major flue-cured tobacco growing countries areArgentina, Brazil, China, India, Tanzania and the U.S. In one aspect,modified tobacco plants or seeds provided herein are in a flue-curedtobacco background selected from the group consisting of CC 13, CC 27,CC 33, CC35, CC 37, CC 65, CC 67, CC 700, GF 318, GL 338, GL 368, GL939, K 346, K 399, K326, NC 102, NC 196, NC 291, NC 297, NC 299, NC 471,NC 55, NC 606, NC 71, NC 72, NC 92, PVH 1118, PVH 1452, PVH 2110,SPEIGHT 168, SPEIGHT 220, SPEIGHT 225, SPEIGHT 227, SPEIGHT 236, and anyvariety essentially derived from any one of the foregoing varieties. Inanother aspect, modified tobacco plants or seeds provided herein are ina flue-cured tobacco background selected from the group consisting ofCoker 48, Coker 176, Coker 371-Gold, Coker 319, Coker 347, GL 939, K149, K326, K 340, K 346, K 358, K 394, K 399, K 730, NC 27NF, NC 37NF,NC 55, NC 60, NC 71, NC 72, NC 82, NC 95, NC 297, NC 606, NC 729, NC2326, McNair 373, McNair 944, Ox 207, Ox 414 NF, Reams 126, Reams 713,Reams 744, RG 8, RG 11, RG 13, RG 17, RG 22, RG 81, RG H4, RG H51,Speight H-20, Speight G-28, Speight G-58, Speight G-70, Speight G-108,Speight G-111, Speight G-117, Speight 168, Speight 179, Speight NF-3, Va116, Va 182, and any variety essentially derived from any one of theforegoing varieties. See WO 2004/041006 A1. In further aspects, modifiedtobacco plants, seeds, hybrids, varieties, or lines provided herein arein any flue cured background selected from the group consisting of K326,K346, and NC196.

Air-cured tobaccos include Burley, Maryland, and dark tobaccos. Thecommon factor is that curing is primarily without artificial sources ofheat and humidity. Burley tobaccos are light to dark brown in color,high in oil, and low in sugar. Burley tobaccos are air-cured in barns.Major Burley growing countries are Argentina, Brazil, Italy, Malawi, andthe U.S. Maryland tobaccos are extremely fluffy, have good burningproperties, low nicotine and a neutral aroma. Major Maryland growingcountries include the U.S. and Italy. In one aspect, modified tobaccoplants or seeds provided herein are in a Burley tobacco backgroundselected from the group consisting of Clay 402, Clay 403, Clay 502, Ky14, Ky 907, Ky 910, Ky 8959, NC 2, NC 3, NC 4, NC 5, NC 2000, TN 86, TN90, TN 97, R 610, R 630, R 711, R 712, NCBH 129, HB4488PLC, PD 7319LC,Bu 21×Ky 10, HBO4P, Ky 14×L 8, Kt 200, Newton 98, Pedigo 561, Pf561 andVa 509. In further aspects, modified tobacco plants, seeds, hybrids,varieties, or lines provided herein are in any Burley backgroundselected from the group consisting of TN 90, KT 209, KT 206, KT212, andHB 4488. In another aspect, modified tobacco plants or seeds providedherein are in a Maryland tobacco background selected from the groupconsisting of Md 10, Md 40, Md 201, Md 609, Md 872 and Md 341.

Dark air-cured tobaccos are distinguished from other types primarily byits curing process which gives dark air-cured tobacco its medium- todark-brown color and distinct aroma. Dark air-cured tobaccos are mainlyused in the production of smokeless tobacco products including chewingtobacco and snuff. In one aspect, modified tobacco plants or seedsprovided herein are in a dark air-cured tobacco background selected fromthe group consisting of Sumatra, Jatim, Dominican Cubano, Besuki, Onesucker, Green River, Virginia sun-cured, and Paraguan Passado.

Dark fire-cured tobaccos are generally cured with low-burning wood fireson the floors of closed curing barns. Dark fire-cured tobaccos are usedfor making pipe blends, cigarettes, chewing tobacco, snuff andstrong-tasting cigars. Major growing regions for dark fire-curedtobaccos are Tennessee, Kentucky, and Virginia, USA. In one aspect,modified tobacco plants or seeds provided herein are in a darkfire-cured tobacco background selected from the group consisting ofNarrow Leaf Madole, Improved Madole, Tom Rosson Madole, Newton's VHMadole, Little Crittenden, Green Wood, Little Wood, Small Stalk BlackMammoth, DT 508, DT 518, DT 592, KY 171, DF 911, DF 485, TN D94, TND950, VA 309, and VA 359.

Oriental tobaccos are also referred to as Greek, aroma and Turkishtobaccos due to the fact that they are typically grown in easternMediterranean regions such as Turkey, Greece, Bulgaria, Macedonia,Syria, Lebanon, Italy, and Romania. The small plant and leaf size,characteristic of today's Oriental varieties, as well as its uniquearoma properties are a result of the plant's adaptation to the poor soiland stressful climatic conditions in which it develop over many pastcenturies. In one aspect, modified tobacco plants or seeds providedherein are in an Oriental tobacco background selected from the groupconsisting of Izmir, Katerini, Samsun, Basma and Krumovgrad, Trabzon,Thesalian, Tasova, Sinop, Izmit, Hendek, Edirne, Semdinli, Adiyanman,Yayladag, Iskenderun, Duzce, Macedonian, Mavra, Prilep, Bafra, Bursa,Bucak, Bitlis, Balikesir, and any variety essentially derived from anyone of the foregoing varieties.

In one aspect, modified tobacco plants, seeds, hybrids, varieties, orlines provided herein are essentially derived from or in the geneticbackground of BU 64, CC 101, CC 200, CC 13, CC 27, CC 33, CC 35, CC 37,CC 65, CC 67, CC 301, CC 400, CC 500, CC 600, CC 700, CC 800, CC 900, CC1063, Coker 176, Coker 319, Coker 371 Gold, Coker 48, CU 263, DF911,Galpão, GL 26H, GL 338, GL 350, GL 395, GL 600, GL 737, GL 939, GL 973,GF 157, GF 318, RJR 901, HB 04P, K 149, K 326, K 346, K 358, K394, K399, K 730, NC 196, NC 37NF, NC 471, NC 55, NC 92, NC2326, NC 95, NC925, PVH 1118, PVH 1452, PVH 2110, PVH 2254, PVH 2275, VA 116, VA 119,KDH 959, KT 200, KT204LC, KY 10, KY 14, KY 160, KY 17, KY 171, KY 907,KY 907LC, KTY14×L8 LC, Little Crittenden, McNair 373, McNair 944, malesterile KY 14×L8, Narrow Leaf Madole, MS KY171, Narrow Leaf Madole(phph), MS Narrow Leaf Madole, MS TND950, PD 7302LC, PD 7305LC, PD7309LC, PD 7312LC, PD 7318LC, PD 7319LC, MSTKS 2002, TKF 2002, TKF 6400,TKF 4028, TKF 4024, KT206LC, KT209LC, KT210LC, KT212LC, NC 100, NC 102,NC 2000, NC 291, NC 297, NC 299, NC 3, NC 4, NC 5, NC 6, NC7, NC 606, NC71, NC 72, NC 810, NC BH 129, NC 2002, Neal Smith Madole, OXFORD 207,‘Perique’, PVH03, PVH09, PVH19, PVH50, PVH51, R 610, R 630, R 7-11, R7-12, RG 17, RG 81, RG H51, RGH 4, RGH 51, RS 1410, Speight 168, Speight172, Speight 179, Speight 210, Speight 220, Speight 225, Speight 227,Speight 234, Speight G-28, Speight G-70, Speight H-6, Speight H20,Speight NF3, TI 1406, TI 1269, TN 86, TN86LC, TN 90, TN90LC, TN 97,TN97LC, TN D94, TN D950, a TR (Tom Rosson) Madole, VA 309, VA 359, orany commercial tobacco variety according to standard tobacco breedingtechniques known in the art.

All foregoing mentioned specific varieties of dark air-cured, Burley,Maryland, dark fire-cured, or Oriental type are only listed forexemplary purposes. Any additional dark air-cured, Burley, Maryland,dark fire-cured, or Oriental varieties are also contemplated in thepresent application.

Also provided herein are populations of tobacco plants described herein.In one aspect, a population of tobacco plants provided herein has aplanting density of between about 5,000 and about 8000, between about5,000 and about 7,600, between about 5,000 and about 7,200, betweenabout 5,000 and about 6,800, between about 5,000 and about 6,400,between about 5,000 and about 6,000, between about 5,000 and about5,600, between about 5,000 and about 5,200, between about 5,200 andabout 8,000, between about 5,600 and about 8,000, between about 6,000and about 8,000, between about 6,400 and about 8,000, between about6,800 and about 8,000, between about 7,200 and about 8,000, or betweenabout 7,600 and about 8,000 plants per acre. In another aspect, apopulation of tobacco plants provided herein is in a soil type with lowto medium fertility.

Also provided herein are containers of tobacco leaves used to store,transport, or otherwise house cured or uncured tobacco leaves fromtobacco plants described herein. As a non-limiting example, a containercan be a box, a bag, a barrel, a crate, or any other suitable container.

Also provided herein are bales of the cured tobacco leaves from tobaccoplants described herein. Also provided herein are bales of the uncuredtobacco leaves from tobacco plants described herein. A bale can be anysize known in the art. A bale can be about 50 pounds, about 75 pounds,about 100 pounds, about 125 pounds, about 150 pounds, about 175 pounds,about 200 pounds, about 225 pounds, about 250 pounds, about 300 pounds,about 350 pounds, about 400 pounds, about 450 pounds, about 500 pounds,about 600 pounds, about 700 pounds, about 800 pounds, about 900 pounds,or about 1000 pounds. A bale can take any shape such as, by anon-limiting example, conical, rectangular, or cuboidal.

Also provided herein are containers of seeds from tobacco plantsdescribed herein. A container of tobacco seeds of the present disclosuremay contain any number, weight, or volume of seeds. For example, acontainer can contain at least, or greater than, about 100, at least, orgreater than, about 200, at least, or greater than, about 300, at least,or greater than, about 400, at least, or greater than, about 500, atleast, or greater than, about 600, at least, or greater than, about 700,at least, or greater than, about 800, at least, or greater than, about900, at least, or greater than, about 1000, at least, or greater than,about 1500, at least, or greater than, about 2000, at least, or greaterthan, about 2500, at least, or greater than, about 3000, at least, orgreater than, about 3500, at least, or greater than, or about 4000 ormore seeds. Alternatively, the container can contain at least, orgreater than, about 1 ounce, at least, or greater than, about 5 ounces,at least, or greater than, about 10 ounces, at least, or greater than,about 1 pound, at least, or greater than, about 2 pounds, at least, orgreater than, about 3 pounds, at least, or greater than, about 4 pounds,at least, or greater than, about 5 pounds or more seeds. Containers oftobacco seeds may be any container available in the art. By way ofnon-limiting example, a container may be a box, a bag, a packet, apouch, a tape roll, a tube, or a bottle.

Also provided herein are containers of tobacco products from tobaccoleaves harvested and cured from tobacco plants described herein. By wayof non-limiting example, a container may be a box, a bag, a packet, apack, a pouch, a tin, or any other container known in the art.

The present disclosure also provides methods for breeding tobacco lines,cultivars, or varieties comprising cured leaf with reduced or eliminatedTSNAs (and, optionally, also comprising increased phenylalanine,increased Chorismate Mutase-like protein activity, increasedantioxidants or decreased nitrite). Breeding can be carried out via anyknown procedures. DNA fingerprinting, SNP mapping, haplotype mapping orsimilar technologies may be used in a marker-assisted selection (MAS)breeding program to transfer or breed a desirable trait or allele into atobacco plant. For example, a breeder can create segregating populationsin an F₂ or backcross generation using F₁ hybrid plants provided hereinor further crossing the F₁ hybrid plants with other donor plants with anagronomically desirable genotype. Plants in the F₂ or backcrossgenerations can be screened for a desired agronomic trait or a desirablechemical profile using one of the techniques known in the art or listedherein. Depending on the expected inheritance pattern or the MAStechnology used, self-pollination of selected plants before each cycleof backcrossing to aid identification of the desired individual plantscan be performed. Backcrossing or other breeding procedure can berepeated until the desired phenotype of the recurrent parent isrecovered. In one aspect, a recurrent parent in the present disclosurecan be a flue-cured variety, a Burley variety, a dark air-cured variety,a dark fire-cured variety, or an Oriental variety. In another aspect, arecurrent parent can be a modified tobacco plant, line, or variety.Other breeding techniques can be found, for example, in Wernsman, E. A.,and Rufty, R. C. 1987. Chapter Seventeen. Tobacco. Pages 669-698 In:Cultivar Development. Crop Species. W. H. Fehr (ed.), MacMillanPublishing Go., Inc., New York, N.Y., incorporated herein by referencein their entirety.

Results of a plant breeding program using modified tobacco plantsdescribed herein includes useful lines, cultivars, varieties, progeny,inbreds, and hybrids of the present disclosure. As used herein, the term“variety” refers to a population of plants that share constantcharacteristics which separate them from other plants of the samespecies. A variety is often, although not always, sold commercially.While possessing one or more distinctive traits, a variety is furthercharacterized by a very small overall variation between individualswithin that variety. A “pure line” variety may be created by severalgenerations of self-pollination and selection, or vegetative propagationfrom a single parent using tissue or cell culture techniques. A varietycan be essentially derived from another line or variety. As defined bythe International Convention for the Protection of New Varieties ofPlants (Dec. 2, 1961, as revised at Geneva on Nov. 10, 1972; on Oct. 23,1978; and on Mar. 19, 1991), a variety is “essentially derived” from aninitial variety if: a) it is predominantly derived from the initialvariety, or from a variety that is predominantly derived from theinitial variety, while retaining the expression of the essentialcharacteristics that result from the genotype or combination ofgenotypes of the initial variety; b) it is clearly distinguishable fromthe initial variety; and c) except for the differences which result fromthe act of derivation, it conforms to the initial variety in theexpression of the essential characteristics that result from thegenotype or combination of genotypes of the initial variety. Essentiallyderived varieties can be obtained, for example, by the selection of anatural or induced mutant, a somaclonal variant, a variant individualfrom plants of the initial variety, backcrossing, or transformation. Afirst tobacco variety and a second tobacco variety from which the firstvariety is essentially derived, are considered as having essentiallyidentical genetic background. A “line” as distinguished from a varietymost often denotes a group of plants used non-commercially, for examplein plant research. A line typically displays little overall variationbetween individuals for one or more traits of interest, although theremay be some variation between individuals for other traits.

In one aspect, the present disclosure provides a method for reducing theamount of one or more Tobacco Specific Nitrosamines (TSNAs) in a curedleaf of a tobacco plant, the method comprising the steps of increasingthe amount of phenylalanine in the tobacco plant via a transgeneencoding or targeting a phenylalanine biosynthetic enzyme, a regulatorof phenylalanine biosynthesis, or a phenylalanine metabolic enzyme; andreducing the amount of one or more TSNAs in a cured leaf of the tobaccoplant or a tobacco product made the cured tobacco leaf.

In one aspect, the present disclosure provides a method for reducing theamount of one or more TSNAs in a cured leaf of a tobacco plant, themethod comprising the steps of increasing the amount of phenylalanine inthe tobacco plant via a genetic modification in an endogenous gene,wherein the endogenous gene encodes a phenylalanine biosynthetic enzyme,a regulator of phenylalanine biosynthesis, or a phenylalanine metabolicenzyme; and reducing the amount of one or more TSNAs in a cured leaf ofthe tobacco plant or a tobacco product made from the cured tobacco leaf.

In one aspect, the present disclosure provides a method for increasingthe amount of one or more anthocyanins in a cured leaf of a tobaccoplant, the method comprising the steps of increasing the amount ofphenylalanine in the tobacco plant via a transgene encoding or targetinga phenylalanine biosynthetic enzyme, a regulator of phenylalaninebiosynthesis, or a phenylalanine metabolic enzyme; and increasing theamount of one or more anthocyanins in a cured leaf of the tobacco plantor a tobacco product made from the cured tobacco leaf.

In one aspect, the present disclosure provides a method for increasingthe amount of one or more anthocyanins in a cured leaf of a tobaccoplant, the method comprising the steps of increasing the amount ofphenylalanine in the tobacco plant via a genetic modification in anendogenous gene, wherein the endogenous gene encodes a phenylalaninebiosynthetic enzyme, a regulator of phenylalanine biosynthesis, or aphenylalanine metabolic enzyme; and increasing the amount of one or moreanthocyanins in a cured leaf of the tobacco plant or a tobacco productmade from the cured tobacco leaf.

In one aspect, the present disclosure provides a method of producing atobacco plant comprising crossing at least one tobacco plant of a firsttobacco variety with at least one tobacco plant of a second tobaccovariety, where the at least one tobacco plant of the first tobaccovariety comprising one or more desired traits, e.g., comprising areduced level of one or more tobacco-specific nitrosamines (TSNAs) incured leaf and further comprising one or more traits selected from thegroup consisting of: a reduced level of nitrite, an increased level ofoxygen radical absorbance capacity (ORAC), and an increased level of oneor more antioxidants, wherein said reduced or increased level iscompared to a control tobacco plant of the same cross grown and curedunder comparable conditions; and selecting for progeny tobacco plantsthat exhibit the one or more desired traits.

In one aspect, a first tobacco variety provided herein comprisesmodified tobacco plants. In another aspect, a second tobacco varietyprovided herein comprises modified tobacco plants. In one aspect, afirst or second tobacco variety is male sterile. In another aspect, afirst or second tobacco variety is cytoplasmically male sterile. Inanother aspect, a first or second tobacco variety is female sterile. Inone aspect, a first or second tobacco variety is an elite variety. Inanother aspect, a first or second tobacco variety is a hybrid.

In one aspect, the present disclosure provides a method of introgressingone or more transgenes or mutations into a tobacco variety, the methodcomprising: (a) crossing a first tobacco variety comprising one or moretransgenes or mutations provided herein with a second tobacco varietywithout the one or more transgenes or mutations to produce one or moreprogeny tobacco plants; (b) genotyping the one or more progeny tobaccoplants for the one or more transgenes or mutations; and (c) selecting aprogeny tobacco plant comprising the one or more transgenes ormutations. In another aspect, these methods further comprisebackcrossing the selected progeny tobacco plant with the second tobaccovariety. In further aspects, these methods further comprise: (d)crossing the selected progeny plant with itself or with the secondtobacco variety to produce one or more further progeny tobacco plants;and (e) selecting a further progeny tobacco plant comprising the one ormore transgenes or mutations. In one aspect, the second tobacco varietyis an elite variety.

In one aspect, the present disclosure provides a method of growing apopulation of modified tobacco plants disclosed herein, where the methodcomprises planting a population of tobacco seeds comprising one or moremutations, one or more transgenes, or both as described herein, wherethe one or more modified tobacco plants or cured leaf of one or moremodified tobacco plants comprise a reduced level of one or more TSNAsand further comprises one or more traits selected from the groupconsisting of an increased level of one or more antioxidants, anincreased level of oxygen radical absorbance capacity (ORAC), and areduced level of nitrite, wherein said reduced or increased level iscompared to control tobacco plants or cured leaf of a control tobaccoplant of the same variety when grown and cured under comparableconditions.

In one aspect, the present disclosure provides a method of growing amodified tobacco plant described herein comprising planting a modifiedtobacco seed described herein; and growing the modified tobacco plantfrom the seed. In an aspect, growing comprises germinating a seed. Inanother aspect, growing comprises placing a seedling in soil, agar,agar-based media, or a hydroponics system. In another aspect, growingcomprises providing a seed or plant with water, light (e.g., artificiallight, sunlight), fertilizer, a rooting media, or a combination thereof.In an aspect, growing can take place indoors (e.g., a greenhouse) oroutdoors (e.g., a field). In one aspect, growing comprises placing aseed or a plant in a container.

In one aspect, this disclosure provides a method for manufacturing amodified seed, comprising introducing a recombinant DNA constructprovided herein into a plant cell; screening a population of plant cellsfor the recombinant DNA construct; selecting one or more plant cellsfrom the population; generating one or more modified plants from the oneor more plant cells; and collecting one or more modified seeds from theone or more modified plants.

As used herein, “locus” is a chromosome region where a polymorphicnucleic acid, trait determinant, gene, or marker is located. The loci ofthis disclosure comprise one or more polymorphisms in a population;e.g., alternative alleles are present in some individuals. As usedherein, “allele” refers to an alternative nucleic acid sequence at aparticular locus. The length of an allele can be as small as 1nucleotide base, but is typically larger. For example, a first allelecan occur on one chromosome, while a second allele occurs on a secondhomologous chromosome, e.g., as occurs for different chromosomes of aheterozygous individual, or between different homozygous or heterozygousindividuals in a population. As used herein, a chromosome in a diploidplant is “hemizygous” when only one copy of a locus is present. Forexample, an inserted transgene is hemizygous when it only inserts intoone sister chromosome (i.e., the second sister chromosome does notcontain the inserted transgene).

In one aspect, a modified plant, seed, plant component, plant cell, orplant genome is homozygous for a transgene provided herein. In anotheraspect, a modified plant, seed, plant component, plant cell, or plantgenome is heterozygous for a transgene provided herein. In one aspect, amodified plant, seed, plant component, plant cell, or plant genome ishemizygous for a transgene provided herein. In one aspect, a modifiedplant, seed, plant component, plant cell, or plant genome is homozygousfor a mutation provided herein. In another aspect, a modified plant,seed, plant component, plant cell, or plant genome is heterozygous for amutation provided herein. In one aspect, a modified plant, seed, plantcomponent, plant cell, or plant genome is hemizygous for a mutationprovided herein.

As used herein, “introgression” or “introgress” refers to thetransmission of a desired allele of a genetic locus from one geneticbackground to another.

As used herein, “crossed” or “cross” means to produce progeny viafertilization (e.g. cells, seeds or plants) and includes crosses betweendifferent plants (sexual) and self-fertilization (selfing).

As used herein, “backcross” and “backcrossing” refer to the processwhereby a progeny plant is repeatedly crossed back to one of itsparents. In a backcrossing scheme, the “donor” parent refers to theparental plant with the desired gene or locus to be introgressed. The“recipient” parent (used one or more times) or “recurrent” parent (usedtwo or more times) refers to the parental plant into which the gene orlocus is being introgressed. The initial cross gives rise to the F₁generation. The term “BC₁” refers to the second use of the recurrentparent, “BC2” refers to the third use of the recurrent parent, and soon. In one aspect, a backcross is performed repeatedly, with a progenyindividual of each successive backcross generation being itselfbackcrossed to the same parental genotype.

As used herein, “elite variety” means any variety that has resulted frombreeding and selection for superior agronomic performance.

As used herein, “selecting” or “selection” in the context of breedingrefer to the act of picking or choosing desired individuals, normallyfrom a population, based on certain pre-determined criteria.

In one aspect, tobacco plants provided herein are hybrid plants. Hybridscan be produced by preventing self-pollination of female parent plants(e.g., seed parents) of a first variety, permitting pollen from maleparent plants of a second variety to fertilize the female parent plants,and allowing F₁ hybrid seeds to form on the female plants.Self-pollination of female plants can be prevented by emasculating theflowers at an early stage of flower development. Alternatively, pollenformation can be prevented on the female parent plants using a form ofmale sterility. For example, male sterility can be produced by malesterility (MS), or transgenic male sterility where a transgene inhibitsmicrosporogenesis and/or pollen formation, or self-incompatibility.Female parent plants containing MS are particularly useful. In aspectsin which the female parent plants are MS, pollen may be harvested frommale fertile plants and applied manually to the stigmas of MS femaleparent plants, and the resulting F₁ seed is harvested. Additionally,female sterile plants can also be used to prevent self-fertilization.

Plants can be used to form single-cross tobacco F₁ hybrids. Pollen froma male parent plant is manually transferred to an emasculated femaleparent plant or a female parent plant that is male sterile to form F₁seed. Alternatively, three-way crosses can be carried out where asingle-cross F₁ hybrid is used as a female parent and is crossed with adifferent male parent. As another alternative, double-cross hybrids canbe created where the F₁ progeny of two different single-crosses arethemselves crossed. Self-incompatibility can be used to particularadvantage to prevent self-pollination of female parents when forming adouble-cross hybrid.

In one aspect, a tobacco variety provided herein is male sterile. Inanother aspect, a tobacco variety provided herein is cytoplasmic malesterile (CMS). Male sterile tobacco plants may be produced by any methodknown in the art. Methods of producing male sterile tobacco aredescribed in Wernsman, E. A., and Rufty, R. C. 1987. Chapter Seventeen.Tobacco. Pages 669-698 In: Cultivar Development. Crop Species. W. H.Fehr (ed.), MacMillan Publishing Go., Inc., New York, N.Y. 761 pp. Inanother aspect, a tobacco variety provided herein is female sterile. Asa non-limiting example, female sterile plants can be made by mutatingthe STIG1 gene. See, for example, Goldman et al. 1994, EMBO Journal13:2976-2984.

As used herein, the term “sequence identity” or “identity” in thecontext of two polynucleotide or polypeptide sequences makes referenceto the residues in the two sequences that are the same when aligned formaximum correspondence over a specified comparison window. Whenpercentage of sequence identity is used in reference to proteins it isrecognized that residue positions which are not identical often differby conservative amino acid substitutions, where amino acid residues aresubstituted for other amino acid residues with similar chemicalproperties (e.g., charge or hydrophobicity) and therefore do not changethe functional properties of the molecule. When sequences differ inconservative substitutions, the percent sequence identity may beadjusted upwards to correct for the conservative nature of thesubstitution. Sequences that differ by such conservative substitutionsare said to have “sequence similarity” or “similarity.”

The use of the term “polynucleotide” is not intended to limit thepresent disclosure to polynucleotides comprising DNA. Those of ordinaryskill in the art will recognize that polynucleotides and nucleic acidmolecules can comprise ribonucleotides and combinations ofribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides andribonucleotides include both naturally occurring molecules and syntheticanalogues. The polynucleotides of the present disclosure also encompassall forms of sequences including, but not limited to, single-strandedforms, double-stranded forms, hairpins, stem-and-loop structures, andthe like.

As used herein, the term “polypeptide” refers to a chain of at least twocovalently linked amino acids.

Nucleic acid molecules, polypeptides, or proteins provided herein can beisolated or substantially purified. An “isolated” or “purified” nucleicacid molecule, polypeptide, protein, or biologically active portionthereof, is substantially or essentially free from components thatnormally accompany or interact with the polynucleotide or protein asfound in its naturally occurring environment. For example, an isolatedor purified polynucleotide or protein is substantially free of othercellular material, or culture medium when produced by recombinanttechniques, or substantially free of chemical precursors or otherchemicals when chemically synthesized. In another aspect, an isolatedpolypeptide provided herein is substantially free of cellular materialin preparations having less than about 30%, less than about 20%, lessthan about 10%, less than about 5%, or less than about 1% (by dryweight) of chemical precursors or non-protein-of-interest chemicals.Fragments of the disclosed polynucleotides and polypeptides encodedthereby are also encompassed by the present invention. Fragments of apolynucleotide may encode polypeptide fragments that retain thebiological activity of the native polypeptide. Alternatively, fragmentsof a polynucleotide that are useful as hybridization probes or PCRprimers using methods known in the art generally do not encode fragmentpolypeptides retaining biological activity. Fragments of apolynucleotide provided herein can range from at least about 20nucleotides, about 50 nucleotides, about 70 nucleotides, about 100nucleotides, about 150 nucleotides, about 200 nucleotides, about 250nucleotides, about 300 nucleotides, and up to the full-lengthpolynucleotide encoding the polypeptides of the invention, depending onthe desired outcome.

Nucleic acids can be isolated using techniques routine in the art. Forexample, nucleic acids can be isolated using any method including,without limitation, recombinant nucleic acid technology, and/or thepolymerase chain reaction (PCR). General PCR techniques are described,for example in PCR Primer: A Laboratory Manual, Dieffenbach & Dveksler,Eds., Cold Spring Harbor Laboratory Press, 1995. Recombinant nucleicacid techniques include, for example, restriction enzyme digestion andligation, which can be used to isolate a nucleic acid. Isolated nucleicacids also can be chemically synthesized, either as a single nucleicacid molecule or as a series of oligonucleotides. Polypeptides can bepurified from natural sources (e.g., a biological sample) by knownmethods such as DEAE ion exchange, gel filtration, and hydroxyapatitechromatography. A polypeptide also can be purified, for example, byexpressing a nucleic acid in an expression vector. In addition, apurified polypeptide can be obtained by chemical synthesis. The extentof purity of a polypeptide can be measured using any appropriate method,e.g., column chromatography, polyacrylamide gel electrophoresis, or HPLCanalysis.

In one aspect, this disclosure provides methods of detecting in plantcells one or more recombinant nucleic acids and polypeptides describedhere. Without being limiting, nucleic acids also can be detected usinghybridization. Hybridization between nucleic acids is discussed indetail in Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual,2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).

Polypeptides can be detected using antibodies. Techniques for detectingpolypeptides using antibodies include enzyme linked immunosorbent assays(ELISAs), Western blots, immunoprecipitations and immunofluorescence. Anantibody provided herein can be a polyclonal antibody or a monoclonalantibody. An antibody having specific binding affinity for a polypeptideprovided herein can be generated using methods well known in the art. Anantibody provided herein can be attached to a solid support such as amicrotiter plate using methods known in the art.

Detection (e.g., of an amplification product, of a hybridizationcomplex, of a polypeptide) can be accomplished using detectable labels.The term “label” is intended to encompass the use of direct labels aswell as indirect labels. Detectable labels include enzymes, prostheticgroups, fluorescent materials, luminescent materials, bioluminescentmaterials, and radioactive materials.

In one aspect, the present disclosure also provides a method of reducingthe level of one or more TSNAs in cured leaf from a tobacco plant, themethod comprising increasing the level of one or more antioxidants inthe tobacco plant by expressing a biosynthetic enzyme, a regulatorytranscription factor, a transporter, a catabolic enzyme, or acombination thereof, for the one or more antioxidants. In anotheraspect, a method comprises expressing a gene promoting the production oraccumulation of one or more antioxidants are selected from the groupconsisting of anthocyanidin, flavanone, flavanol, flavone, flavonol,isoflavone, hydroxybenzoic acid, hydroxycinnamic acid, ellagitannin,stibene, lignan, carotenoids, and glycyrrhzin. In a further aspect, amethod comprises expressing a gene promoting the production oraccumulation of one or more antioxidants are selected from the groupconsisting of Delphnidin, Cyanidin, Procyanidin, Prodelphinidin,Hesperetin, Perlargonidin, Peonidin, Petunidin, Naringenin, Catechin,Epicatechin, Apigenin, Luteonin, Quercetin, Myricetin, Rutin, Genistein,Daidzein, Gallic acid, Vanillic acid, Protocatechuic acid, Ferunic acid,Cinnamic acid, Coumeric acid, Chlorogenic acid, Coffeic acid, ferulicacid, Sanguiin, Resveratrol, Sesamin, Caretonoids, and Vitamin C. In oneaspect, a method does not substantially reduce the level of totalalkaloids in the tobacco plant. In another aspect, a method does notsubstantially reduce the level of nicotine in the tobacco plant.

In one aspect, the present disclosure provides a method for reducing thelevel of one or more TSNAs in cured tobacco leaf or a tobacco productmade therefrom, the method comprising increasing the level of one ormore antioxidants in a tobacco plant via a transgene encoding ordirectly modulating an antioxidant biosynthetic enzyme, a regulatorytranscription factor of an antioxidant, an antioxidant transporter, anantioxidant metabolic enzyme, or a combination thereof; and reducing thelevel of one or more TSNAs in cured tobacco leaf from the tobacco plantor a tobacco product made from the cured tobacco leaf.

In another aspect of a method described herein, a modified tobacco plantor leaf provided here has a similar leaf chemistry profile compared to acontrol plant when grown and cured under comparable conditions. Withoutbeing limiting, a leaf chemistry profile can comprise the amount ofalkaloids (e.g., nicotine, nornicotine, anabasine, anatabine), malicacid, and reducing sugars (e.g., dextrose), or a combination thereof ina tobacco plant or tobacco leaf. In another aspect of a method describedherein, a modified plant or leaf provided herein comprises a totalalkaloids level within about 90%, within about 80%, within about 70%,within about 60%, within about 50%, within about 45%, within about 40%,within about 35%, within about 30%, within about 25%, within about 20%,within about 15%, within about 10%, within about 5%, within about 4%,within about 3%, within about 2%, within about 1%, or within about 0.5%of the total alkaloids level of a control plant when grown and curedunder comparable conditions. In another aspect of a method describedherein, a modified plant or leaf provided herein comprises a totalalkaloids level that is reduced by at least 1%, at least 5%, at least10%, at least 15%, at least 20%, at least 25%, at least 30%, at least35%, at least 40%, at least 45%, at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, or at least 95% compared to a control plant whengrown and cured under comparable conditions. In another aspect of amethod described herein, a modified plant or leaf provided hereincomprises a nicotine level within about 90%, within about 80%, withinabout 70%, within about 60%, within about 50%, within about 45%, withinabout 40%, within about 35%, within about 30%, within about 25%, withinabout 20%, within about 15%, within about 10%, within about 5%, withinabout 4%, within about 3%, within about 2%, within about 1%, or withinabout 0.5% of the nicotine level of a control plant when grown and curedunder comparable conditions. In another aspect of a method describedherein, a modified plant or leaf provided herein comprises a nornicotinelevel within about 50%, within about 45%, within about 40%, within about35%, within about 30%, within about 25%, within about 20%, within about15%, within about 10%, within about 5%, within about 4%, within about3%, within about 2%, within about 1%, or within about 0.5% of thenornicotine level of a control plant when grown and cured undercomparable conditions. In another aspect of a method described herein, amodified plant or leaf provided herein comprises an anabasine levelwithin about 50%, within about 45%, within about 40%, within about 35%,within about 30%, within about 25%, within about 20%, within about 15%,within about 10%, within about 5%, within about 4%, within about 3%,within about 2%, within about 1%, or within about 0.5% of the anabasinelevel of a control plant when grown and cured under comparableconditions. In another aspect of a method described herein, a modifiedplant or leaf provided herein comprises an anatabine level within about50%, within about 45%, within about 40%, within about 35%, within about30%, within about 25%, within about 20%, within about 15%, within about10%, within about 5%, within about 4%, within about 3%, within about 2%,within about 1%, or within about 0.5% of the anatabine level of acontrol plant when grown and cured under comparable conditions. Inanother aspect of a method described herein, a modified plant or leafprovided herein comprises a malic acid level within about 50%, withinabout 45%, within about 40%, within about 35%, within about 30%, withinabout 25%, within about 20%, within about 15%, within about 10%, withinabout 5%, within about 4%, within about 3%, within about 2%, withinabout 1%, or within about 0.5% of the malic acid level of a controlplant when grown and cured under comparable conditions. In anotheraspect of a method described herein, a modified plant or leaf providedherein comprises a reducing sugars level within about 50%, within about45%, within about 40%, within about 35%, within about 30%, within about25%, within about 20%, within about 15%, within about 10%, within about5%, within about 4%, within about 3%, within about 2%, within about 1%,or within about 0.5% of the reducing sugars level of a control plantwhen grown and cured under comparable conditions. In another aspect of amethod described herein, a modified plant or leaf provided hereincomprises a dextrose level within about 50%, within about 45%, withinabout 40%, within about 35%, within about 30%, within about 25%, withinabout 20%, within about 15%, within about 10%, within about 5%, withinabout 4%, within about 3%, within about 2%, within about 1%, or withinabout 0.5% of the dextrose level of a control plant when grown and curedunder comparable conditions.

In another aspect of a method described herein, the level of one or moreTSNAs reduces by at least 50%, by at least 45%, by at least 40%, by atleast 35%, by at least 30%, by at least 25%, by at least 20%, by atleast 15%, by at least 10%, or by at least 5%, compared to cured leaffrom a control tobacco plant not comprising a transgene. In a furtheraspect of a method described herein, cured leaf of the modified tobaccoplant produces or comprises less than 2, less than 1.9, less than 1.8,less than 1.7, less than 1.6, less than 1.5, less than 1.4, less than1.3, less than 1.2, less than 1.1, less than 1.0, less than 0.9, lessthan 0.8, less than 0.7, less than 0.6, less than 0.5, less than 0.4,less than 0.3, less than 0.2, less than 0.15, less than 0.1, or lessthan 0.05 ppm total TSNAs. In a further aspect of a method describedherein, cured leaf of the modified tobacco plant comprises between 2 and0.05, between 1.9 and 0.05, between 1.8 and 0.05, between 1.7 and 0.05,between 1.6 and 0.05, between 1.5 and 0.05, between 1.4 and 0.05,between 1.3 and 0.05, between 1.2 and 0.05, between 1.1 and 0.05,between 1.0 and 0.05, between 0.9 and 0.05, between 0.8 and 0.05,between 0.7 and 0.05, between 0.6 and 0.05, between 0.5 and 0.05,between 0.4 and 0.05, between 0.3 and 0.05, between 0.2 and 0.05,between 0.15 and 0.05, or between 0.1 and 0.05 ppm total TSNAs. In afurther aspect of a method described herein, cured leaf of the modifiedtobacco plant comprises between 2 and 0.05, between 1.8 and 0.1, between1.5 and 0.15, between 1.2 and 0.2, between 1.0 and 0.3, between 0.8 and0.4, or between 0.6 and 0.5 ppm total TSNAs. In a further aspect of amethod described herein, one or more TSNAs are selected from the groupconsisting of N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT), N′-nitrosoanabasine (NAB), and any combination thereof. In afurther aspect of a method described herein, the TSNA reductioncomprises a reduction of NNK. In a further aspect of a method describedherein, the TSNA reduction consists of a reduction of NNK. In a furtheraspect of a method described herein, NNK is reduced below 0.08 parts permillion, below 0.07 parts per million, below 0.06 parts per million, orbelow 0.05 parts per million, as measured in freeze-dried cured leafsamples using liquid chromatography with tandem mass spectrometry.

In another aspect of a method described herein, the tobacco plantcomprises reduced nicotine demethylase activity compared to a controlplant. In a further aspect of a method described herein, the tobaccoplant comprises at least one mutation in a nicotine demethylase geneselected from the group consisting of CYP82E4, CYP82E5, CYP82E10, and acombination thereof. In another aspect of a method described herein, amethod reduces nitrite levels in cured tobacco leaf comprising thetransgene. In another aspect of a method described herein, a methodincreases the oxygen radical absorbance capacity level in cured tobaccoleaf comprising the transgene. In another aspect of a method describedherein, the one or more antioxidants that are increased in cured tobaccoleaf comprising the transgene are selected from the group consisting ofanthocyanidin, flavanone, flavanol, flavone, flavonol, isoflavone,hydroxybenzoic acid, hydroxycinnamic acid, ellagitannin, stibene,lignan, carotenoids, and glycyrrhzin. In a further aspect of a methoddescribed herein, the one or more antioxidants that are increased incured tobacco leaf comprising the transgene are selected from the groupconsisting of Delphnidin, Cyanidin, Procyanidin, Prodelphinidin,Hesperetin, Perlargonidin, Peonidin, Petunidin, Naringenin, Catechin,Epicatechin, Apigenin, Luteonin, Quercetin, Myricetin, Rutin, Genistein,Daidzein, Gallic acid, Vanillic acid, Protocatechuic acid, Ferunic acid,Cinnamic acid, Coumeric acid, Chlorogenic acid, Coffeic acid, ferulicacid, Sanguiin, Resveratrol, Sesamin, Caretonoids, and Vitamin C In afurther aspect of a method described herein, a method does notsubstantially reduce the level of total alkaloids in a tobacco plant. Ina further aspect of a method described herein, a method does notsubstantially reduce the level of nicotine in a tobacco plant. In anaspect of a method described herein, a transgene encodes or directlymodulates a biosynthetic enzyme, a regulatory transcription factor, atransporter, a metabolic enzyme, or a combination thereof, for one ormore antioxidants selected from the group consisting of anthocyanidin,flavanone, flavanol, flavone, flavonol, isoflavone, hydroxybenzoic acid,hydroxycinnamic acid, ellagitannin, stibene, lignan, carotenoids, andglycyrrhzin. In a further aspect of a method described herein, atransgene encodes or directly modulates a biosynthetic enzyme, aregulatory transcription factor, a transporter, a metabolic enzyme, or acombination thereof, for one or more antioxidants selected from thegroup consisting of Delphnidin, Cyanidin, Procyanidin, Prodelphinidin,Hesperetin, Perlargonidin, Peonidin, Petunidin, Catechin, Epicatechin,Apigenin, Luteonin, Quercetin, Myricetin, Rutin, Genistein, Daidzein,Gallic acid, Vanillic acid, Protocatechuic acid, Ferunic acid, Cinnamicacid, Coumeric acid, Chlorogenic acid, Coffeic acid, ferulic acid,Sanguiin, Resveratrol, Sesamin, Caretonoids, and Vitamin C In anotheraspect of a method described herein, the transgene encodes a proteincomprising a sequence having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, 99%, or 100% identity to a sequence selectedfrom the group consisting of SEQ ID Nos: 1 to 23, 47 to 52, 64 to 65,and 68 to 70.

In one aspect, the present disclosure provides a method for reducing thelevel of one or more TSNAs in cured tobacco leaf or a tobacco productmade therefrom, a method comprising increasing the level of one or moreantioxidants in a tobacco plant via a genetic modification in anendogenous gene, wherein the endogenous gene encodes an antioxidantbiosynthetic enzyme, a regulatory transcription factor of anantioxidant, an antioxidant transporter, an antioxidant metabolicenzyme, or a combination thereof; and reducing the level of one or moreTSNAs in cured tobacco leaf from the tobacco plant or a tobacco productmade from the cured tobacco leaf. In another aspect of a methoddescribed herein, the level of one or more TSNAs is reduced by at least50%, by at least 45%, by at least 40%, by at least 35%, by at least 30%,by at least 25%, by at least 20%, by at least 15%, by at least 10%, orby at least 5%, compared to cured leaf from a control tobacco plant notcomprising a transgene. In a further aspect of a method describedherein, one or more TSNAs are selected from the group consisting ofN′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) N′-nitrosoanabasine (NAB), and any combination thereof. In furtheraspect of a method described herein, the TSNA reduction comprises areduction of NNK. In a further aspect of a method described herein, theTSNA reduction consists of a reduction of NNK. In a further aspect of amethod described herein, NNK is reduced below 0.08 parts per million asmeasured in freeze-dried cured leaf samples using liquid chromatographywith tandem mass spectrometry.

In another aspect of a method described herein, a tobacco plantcomprises reduced nicotine demethylase activity compared to a controlplant. In a further aspect of a method described herein, a tobacco plantcomprises at least one mutation in a nicotine demethylase gene selectedfrom the group consisting of CYP82E4, CYP82E5, CYP82E10, and acombination thereof. In another aspect of a method described herein, amethod reduces nitrite levels in cured tobacco leaf comprising atransgene. In another aspect of a method described herein, a methodincreases the oxygen radical absorbance capacity level in cured tobaccoleaf comprising a transgene. In another aspect of a method describedherein, a method increases the oxygen radical absorbance capacity levelin cured tobacco leaf comprising a transgene. In another aspect of amethod described herein, one or more increased antioxidants are tobacconative antioxidants. In another aspect of a method described herein, theone or more antioxidants that are increased in cured tobacco leafcomprising a transgene are selected from the group consisting ofanthocyanidin, flavanone, flavanol, flavone, flavonol, isoflavone,hydroxybenzoic acid, hydroxycinnamic acid, ellagitannin, stibene,lignan, carotenoids, and glycyrrhzin. In a further aspect of the method,the one or more antioxidants that are increased in cured tobacco leafcomprising the transgene are selected from the group consisting ofDelphnidin, Cyanidin, Procyanidin, Prodelphinidin, Hesperetin,Perlargonidin, Peonidin, Petunidin, Naringenin, Catechin, Epicatechin,Apigenin, Luteonin, Quercetin, Myricetin, Rutin, Genistein, Daidzein,Gallic acid, Vanillic acid, Protocatechuic acid, Ferunic acid, Cinnamicacid, Coumeric acid, Chlorogenic acid, Coffeic acid, ferulic acid,Sanguiin, Resveratrol, Sesamin, Caretonoids, and Vitamin C.

In a further aspect of a method described herein, a method does notsubstantially reduce the level of total alkaloids in a tobacco plant. Ina further aspect of a method described herein, a method does notsubstantially reduce the level of nicotine in a tobacco plant. Inanother aspect of a method described herein, an endogenous gene encodesa protein comprising a sequence having at least 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% identity to a sequenceselected from the group consisting of SEQ ID Nos: 1 to 23, 47 to 52, 64to 65, and 68 to 70.

In one aspect, the present disclosure provides a method formanufacturing a tobacco product, the method comprising obtaining curedtobacco leaf comprising a transgene or comprising a genetic modificationin an endogenous gene, and further comprising an increased level of oneor more antioxidants compared to cured tobacco leaf control lacking atransgene or a genetic modification, wherein an endogenous gene encodesan antioxidant biosynthetic enzyme, a regulatory transcription factor ofan antioxidant, an antioxidant transporter, an antioxidant metabolicenzyme, or a combination thereof, wherein a transgene encodes ordirectly modulates an antioxidant biosynthetic enzyme, a regulatorytranscription factor of an antioxidant, an antioxidant transporter, anantioxidant metabolic enzyme, or a combination thereof; and producing atobacco product from cured tobacco leaf, wherein a tobacco productcomprises a reduced level of one or more TSNAs relative to a controltobacco product prepared from a control cured tobacco leaf. In anotheraspect of a method described herein, cured tobacco leaf comprises atransgene encoding or directly modulating an antioxidant biosyntheticenzyme, a regulatory transcription factor of an antioxidant, anantioxidant transporter, an antioxidant metabolic enzyme, or acombination thereof. In another aspect of a method described herein,cured tobacco leaf comprises a genetic modification in an antioxidantbiosynthetic enzyme, a regulatory transcription factor of anantioxidant, an antioxidant transporter, an antioxidant metabolicenzyme, or a combination thereof.

In another aspect of a method described herein, the level of one or moreTSNAs is reduced by at least 50%, by at least 45%, by at least 40%, byat least 35%, by at least 30%, by at least 25%, by at least 20%, by atleast 15%, by at least 10%, or by at least 5%, compared to cured leaffrom a control tobacco plant not comprising a transgene. In anotheraspect of a method described herein, the level of one or more TSNAs isreduced by at least 50%, by at least 45%, by at least 40%, by at least35%, by at least 30%, by at least 25%, by at least 20%, by at least 15%,by at least 10%, or by at least 5%, compared to cured leaf from acontrol tobacco plant not comprising a genetic modification in anendogenous gene. In another aspect of a method described herein, curedtobacco leaf comprises a reduced nitrite level compared to a controlplant without a transgene. In another aspect of a method describedherein, the cured tobacco leaf comprises a reduced nitrite levelcompared to a control plant without a genetic modification in anendogenous gene. In another aspect of a method described herein, curedtobacco leaf comprises an increased amount of phenylalanine compared toa control plant without a transgene. In another aspect of a methoddescribed herein, cured tobacco leaf comprises an increased amount ofphenylalanine compared to a control plant without a genetic modificationin an endogenous gene.

In one aspect, the present disclosure provides a method for preparingcured tobacco leaf, the method comprising growing a tobacco plantcomprising a transgene or a genetic modification in an endogenous gene,and further comprising an increased level of one or more antioxidantscompared to a control cured tobacco leaf lacking a transgene or agenetic modification, wherein an endogenous gene encodes an antioxidantbiosynthetic enzyme, a regulatory transcription factor of anantioxidant, an antioxidant transporter, an antioxidant metabolicenzyme, or a combination thereof, wherein a transgene encodes ordirectly modulates an antioxidant biosynthetic enzyme, a regulatorytranscription factor of an antioxidant, an antioxidant transporter, anantioxidant metabolic enzyme, or a combination thereof; and preparingcured leaf from a tobacco plant, wherein cured leaf comprises a reducedlevel of one or more TSNAs relative to a control cured leaf from acontrol tobacco plant not comprising a transgene or a geneticmodification. In another aspect of a method described herein, curedtobacco leaf comprises a transgene encoding or directly modulating anantioxidant biosynthetic enzyme, a regulatory transcription factor of anantioxidant, an antioxidant transporter, an antioxidant metabolicenzyme, or a combination thereof. In another aspect of a methoddescribed herein, cured tobacco leaf comprises a genetic modification inan antioxidant biosynthetic enzyme, a regulatory transcription factor ofan antioxidant, an antioxidant transporter, an antioxidant metabolicenzyme, or a combination thereof.

In another aspect of a method described herein, the level of one or moreTSNAs is reduced by at least 50%, by at least 45%, by at least 40%, byat least 35%, by at least 30%, by at least 25%, by at least 20%, by atleast 15%, by at least 10%, or by at least 5%, compared to cured leaffrom a control tobacco plant not comprising a transgene. In anotheraspect of a method described herein, the level of one or more TSNAs isreduced by at least 50%, by at least 45%, by at least 40%, by at least35%, by at least 30%, by at least 25%, by at least 20%, by at least 15%,by at least 10%, or by at least 5%, compared to cured leaf from acontrol tobacco plant not comprising a genetic modification in anendogenous gene. In another aspect of a method described herein, curedtobacco leaf comprises a reduced nitrite level compared to a controlplant without a transgene. In another aspect of a method describedherein, cured tobacco leaf comprises a reduced nitrite level compared toa control plant without a genetic modification in an endogenous gene. Inanother aspect of a method described herein, cured tobacco leafcomprises an increased amount of phenylalanine compared to a controlplant without a transgene. In another aspect of a method describedherein, cured tobacco leaf comprises an increased amount ofphenylalanine compared to a control plant without a genetic modificationin an endogenous gene.

In one aspect, the present disclosure provides cured leaf of a modifiedtobacco plant, wherein cured leaf comprises a reduced level of one ormore tobacco-specific nitrosamines (TSNAs) and further comprises anincreased level of one or more antioxidants and a reduced nitrite level,wherein reduced and increased levels are compared to a control curedleaf of an unmodified tobacco plant of the same variety when grown andcured under comparable conditions, wherein a modification comprises atransgene or a genetic modification in an endogenous gene, wherein atransgene or an endogenous gene encodes an antioxidant biosyntheticenzyme, a regulatory transcription factor of an antioxidant, anantioxidant transporter, an antioxidant metabolic enzyme, or acombination thereof; wherein a modified tobacco plant does not comprisea transgene overexpressing an Arabidopsis PAP1 protein.

In a further aspect of a method described herein, cured leaf of themodified tobacco plant produces or comprises less than 2, less than 1.9,less than 1.8, less than 1.7, less than 1.6, less than 1.5, less than1.4, less than 1.3, less than 1.2, less than 1.1, less than 1.0, lessthan 0.9, less than 0.8, less than 0.7, less than 0.6, less than 0.5,less than 0.4, less than 0.3, less than 0.2, less than 0.15, less than0.1, or less than 0.05 ppm total TSNAs. In a further aspect of a methoddescribed herein, cured leaf of the modified tobacco plant comprisesbetween 2 and 0.05, between 1.9 and 0.05, between 1.8 and 0.05, between1.7 and 0.05, between 1.6 and 0.05, between 1.5 and 0.05, between 1.4and 0.05, between 1.3 and 0.05, between 1.2 and 0.05, between 1.1 and0.05, between 1.0 and 0.05, between 0.9 and 0.05, between 0.8 and 0.05,between 0.7 and 0.05, between 0.6 and 0.05, between 0.5 and 0.05,between 0.4 and 0.05, between 0.3 and 0.05, between 0.2 and 0.05,between 0.15 and 0.05, or between 0.1 and 0.05 ppm total TSNAs. In afurther aspect of a method described herein, cured leaf of the modifiedtobacco plant comprises between 2 and 0.05, between 1.8 and 0.1, between1.5 and 0.15, between 1.2 and 0.2, between 1.0 and 0.3, between 0.8 and0.4, or between 0.6 and 0.5 ppm total TSNAs. In a further aspect of amethod described herein, one or more TSNAs are selected from the groupconsisting of N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) N′-nitrosoanabasine (NAB), and any combination thereof. In afurther aspect of a method described herein, the TSNA reductioncomprises a reduction of NNK. In a further aspect of a method describedherein, the TSNA reduction consists of a reduction of NNK. In a furtheraspect of a method described herein, NNK is reduced below 0.08 parts permillion, below 0.07 parts per million, below 0.06 parts per million, orbelow 0.05 parts per million, as measured in freeze-dried cured leafsamples using liquid chromatography with tandem mass spectrometry. Inanother aspect of a method described herein, a tobacco plant comprisesreduced nicotine demethylase activity compared to a control plant. In afurther aspect of a method described herein, a tobacco plant comprisesat least one mutation in a nicotine demethylase gene selected from thegroup consisting of CYP82E4, CYP82E5, CYP82E10, and a combinationthereof. In a further aspect of a method described herein, a methodprovides a tobacco product comprising cured leaf of a modified tobaccoplant.

Having now generally described the disclosure, the same will be morereadily understood through reference to the following examples that areprovided by way of illustration, and are not intended to be limiting ofthe present disclosure, unless specified.

The following are exemplary embodiments of the present disclosure.

Embodiment 1. A method for reducing the amount of one or more TobaccoSpecific Nitrosamines (TSNAs) in a cured leaf of a tobacco plant, saidmethod comprising the steps of:

increasing the amount of phenylalanine in said tobacco plant via atransgene encoding or targeting a phenylalanine biosynthetic enzyme, aregulator of phenylalanine biosynthesis, or a phenylalanine metabolicenzyme; and

reducing the amount of said one or more TSNAs in a cured leaf of saidtobacco plant or a tobacco product made from said cured tobacco leaf.

Embodiment 2. A method for reducing the amount of one or more TSNAs in acured leaf of a tobacco plant, said method comprising the steps of:

increasing the amount of phenylalanine in said tobacco plant via agenetic modification in an endogenous gene, wherein said endogenous geneencodes a phenylalanine biosynthetic enzyme, a regulator ofphenylalanine biosynthesis, or a phenylalanine metabolic enzyme; and

reducing the amount of said one or more TSNAs in a cured leaf of saidtobacco plant or a tobacco product made from said cured tobacco leaf.

Embodiment 3. A method for increasing the amount of one or moreanthocyanins in a cured leaf of a tobacco plant, said method comprisingthe steps of:

increasing the amount of phenylalanine in said tobacco plant via atransgene encoding or targeting a phenylalanine biosynthetic enzyme, aregulator of phenylalanine biosynthesis, or a phenylalanine metabolicenzyme; and

increasing the amount of one or more anthocyanins in a cured leaf ofsaid tobacco plant or a tobacco product made from said cured tobaccoleaf.

Embodiment 4. A method for increasing the amount of one or moreanthocyanins in a cured leaf of a tobacco plant, said method comprisingthe steps of:

increasing the amount of phenylalanine in said tobacco plant via agenetic modification in an endogenous gene, wherein said endogenous geneencodes a phenylalanine biosynthetic enzyme, a regulator ofphenylalanine biosynthesis, or a phenylalanine metabolic enzyme; and

increasing the amount of one or more anthocyanins in a cured leaf ofsaid tobacco plant or a tobacco product made from said cured tobaccoleaf.

Embodiment 5. The method of any one of embodiments 1 to 4, wherein saidmethod further comprises reducing the amount of total alkaloids by atleast 10% in a cured leaf compared to a cured tobacco leaf or a tobaccoproduct from a control tobacco plant not comprising said modification.

Embodiment 6. The method of embodiment 1 or 2, wherein the amount ofsaid one or more TSNAs is reduced by at least 50% compared to a curedtobacco leaf or a tobacco product from a control tobacco plant notcomprising said transgene.

Embodiment 7. The method of embodiment 1 or 2, wherein said curedtobacco leaf comprises less than 2 ppm total TSNAs.

Embodiment 8. The method of embodiment 1 or 2, wherein said curedtobacco leaf comprises between 2 and 0.05 ppm total TSNAs.

Embodiment 9. The method of embodiment 1 or 2, wherein said curedtobacco leaf comprises less than 0.08 ppm4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), wherein the levelof said total TSNAs is measured based on a freeze-dried cured leafsample using liquid chromatograph with tandem mass spectrometry(LC/MS/MS).

Embodiment 10. The method of embodiment 1 or 2, wherein said one or moretobacco-specific nitrosamines (TSNAs) are selected from the groupconsisting of N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) N′-nitrosoanabasine (NAB), and any combination thereof.

Embodiment 11. The method of embodiment 3 or 4, wherein said one or moreanythocyanins is selected from the group consisting of Delphnidin,Cyanidin, Procyanidin, Prodelphinidin, Hesperetin, Perlargonidin,Peonidin, and Petunidin.

Embodiment 12. The method of embodiment 3 or 4, further comprising thestep of reducing the amount of said one or more TSNAs in a cured leaf ofsaid tobacco plant or a tobacco product made from said cured tobaccoleaf.

Embodiment 13. The method of embodiment 12, wherein the amount of saidone or more TSNAs is reduced by at least 50% compared to a cured tobaccoleaf or a tobacco product from a control tobacco plant not comprisingsaid transgene.

Embodiment 14. The method of embodiment 12, wherein said cured tobaccoleaf comprises less than 2 ppm total TSNAs.

Embodiment 15. The method of embodiment 12, wherein said cured tobaccoleaf comprises between 2 and 0.05 ppm total TSNAs.

Embodiment 16. The method of embodiment 12, wherein said cured tobaccoleaf comprises less than 0.08 ppm4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), wherein the levelof said total TSNAs is measured based on a freeze-dried cured leafsample using liquid chromatograph with tandem mass spectrometry(LC/MS/MS).

Embodiment 17. The method of embodiment 12, wherein said one or moretobacco-specific nitrosamines (TSNAs) are selected from the groupconsisting of N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) N′-nitrosoanabasine (NAB), and any combination thereof.

Embodiment 18. The method of any one of embodiments 1 to 4, wherein saidregulator of phenylalanine biosynthesis is a regulatory transcriptionfactor.

Embodiment 19. The method of any one of embodiments 1 to 4, wherein saidcured leaf of a tobacco plant is selected from the group consisting ofair-cured Burley tobacco, air-cured dark tobacco, fire-cured darktobacco, and Oriental tobacco.

Embodiment 20. The method of any one of embodiments 1 to 4, wherein saidtobacco plant is selected from the group consisting of a flue-curedvariety, a Burley variety, a Maryland variety, a dark variety, and anOriental variety.

Embodiment 21. The method of any one of embodiments 1 to 4, furthercomprising increasing the amount of one or more antioxidants in saidcured leaf of a tobacco plant.

Embodiment 22. The method of embodiment 21, wherein said one or moreantioxidants are selected from the group consisting of flavanone,flavanol, flavone, flavonol, isoflavone, hydroxybenzoic acid,hydroxycinnamic acid, ellagitannin, stibene, lignan, carotenoids, andglycyrrhzin.

Embodiment 23. The method of embodiment 21, wherein said one or moreantioxidants are selected from the group consisting of Naringenin,Catechin, Epicatechin, Apigenin, Luteonin, Quercetin, Myricetin, Rutin,Genistein, Daidzein, Gallic acid, Vanillic acid, Protocatechuic acid,Ferunic acid, Cinnamic acid, Coumeric acid, Chlorogenic acid, Coffeicacid, ferulic acid, Sanguiin, Resveratrol, Sesamin, Caretonoids, andVitamin C.

Embodiment 24. The method of embodiments 1 or 3, wherein said transgeneencodes a chorismate mutase-like polypeptide.

Embodiment 25. The method of embodiment 24, wherein said chorismatemutase-like polypeptide has at least 80% homology to a sequence selectedfrom the group consisting of SEQ ID NOs: 68 to 70.

Embodiment 26. The method of embodiment 24, wherein said chorismatemutase-like polypeptide comprises a sequence selected from the groupconsisting of SEQ ID NOs: 68 to 70.

Embodiment 27. The method of embodiment 24, wherein said chorismatemutase-like polypeptide is encoded by a polynucleotide sequence havingat least 80% homology to a sequence selected from the group consistingof SEQ ID NOs: 71 to 73.

Embodiment 28. The method of embodiment 24, wherein said chorismatemutase-like polypeptide is encoded by a polynucleotide sequence selectedfrom the group consisting of SEQ ID NOs: 71 to 73.

Embodiment 29. The method of embodiments 2 or 4, wherein said endogenousgene encodes a chorismate mutase-like polypeptide.

Embodiment 30. The method of embodiment 29, wherein said chorismatemutase-like polypeptide has at least 80% homology to a sequence selectedfrom the group consisting of SEQ ID NOs: 68 to 70.

Embodiment 31. The method of embodiment 29, wherein said chorismatemutase-like polypeptide comprises a sequence selected from the groupconsisting of SEQ ID NOs: 68 to 70.

Embodiment 32. The method of embodiment 29, wherein said chorismatemutase-like polypeptide is encoded by a polynucleotide sequence havingat least 80% homology to a sequence selected from the group consistingof SEQ ID NOs: 71 to 73.

Embodiment 33. The method of embodiment 29, wherein said chorismatemutase-like polypeptide is encoded by a polynucleotide sequence selectedfrom the group consisting of SEQ ID NOs: 71 to 73.

Embodiment 34. The method of embodiment 21, wherein said tobacco plantfurther comprises a transgene encoding or targeting an antioxidantbiosynthetic enzyme, a regulatory transcription factor of anantioxidant, an antioxidant transporter, an antioxidant metabolicenzyme.

Embodiment 35. The method of embodiment 34, wherein said transgeneencodes or targets a biosynthetic enzyme, a regulatory transcriptionfactor, a transporter, a metabolic enzyme, or a combination thereof, forone or more antioxidants selected from the group consisting offlavanone, flavanol, flavone, flavonol, isoflavone, hydroxybenzoic acid,hydroxycinnamic acid, ellagitannin, stibene, lignan, carotenoids, andglycyrrhzin.

Embodiment 36. The method of embodiment 34, wherein said transgeneencodes or targets a biosynthetic enzyme, a regulatory transcriptionfactor, a transporter, a metabolic enzyme, or a combination thereof, forone or more antioxidants selected from the group consisting ofNaringenin, Catechin, Epicatechin, Apigenin, Luteonin, Quercetin,Myricetin, Rutin, Genistein, Daidzein, Gallic acid, Vanillic acid,Protocatechuic acid, Ferunic acid, Cinnamic acid, Coumeric acid,Chlorogenic acid, Coffeic acid, ferulic acid, Sanguiin, Resveratrol,Sesamin, Caretonoids, and Vitamin C.

Embodiment 37. The method of embodiment 34, wherein said transgeneencodes a protein comprising a sequence having at least 80% identity toa sequence selected from the group consisting of SEQ ID Nos. 1 to 23, 47to 52, and 64 to 65.

Embodiment 38. The method of embodiment 34, wherein said endogenous geneencodes a protein comprising a sequence having at least 80% identity toa sequence selected from the group consisting of SEQ ID Nos. 1 to 23, 47to 52, and 64 to 65.

Embodiment 39. A cured tobacco leaf of a modified tobacco plant, whereinsaid cured tobacco leaf comprises a decreased amount of one or moreTSNAs and an increased amount of at least one Chorismate Mutase-likepolypeptide, wherein said decreased and increased amounts are comparedto an unmodified control tobacco plant.

Embodiment 40. A cured tobacco leaf of a modified tobacco plant, whereinsaid cured tobacco leaf comprises a decreased amount of one or moreTSNAs and an increased amount of phenylalanine, wherein said decreasedand increased amounts are compared to an unmodified control tobaccoplant.

Embodiment 41. A cured tobacco leaf of a modified tobacco plant, whereinsaid cured tobacco leaf comprises a decreased amount of one or moreTSNAs and an increased amount of one or more phenylalanine biosyntheticenzymes, regulators of phenylalanine biosynthesis, or phenylalaninemetabolic enzymes, wherein said decreased and increased amounts arecompared to an unmodified control tobacco plant.

Embodiment 42. The cured tobacco leaf of any one of embodiments 39 to41, further comprising a reduced amount of total alkaloids that is aleast 10% less than the total amount of alkaloids in an unmodifiedcontrol tobacco plant.

Embodiment 43. The cured tobacco leaf of any one of embodiments 39 to41, further comprising an increased amount of at least one polypeptidehaving at least 80% homology a sequence selected from the groupconsisting of SEQ ID Nos. 1 to 23, 47 to 52, and 64 to 65.

Embodiment 44. The cured tobacco leaf of any one of embodiments 39 to41, further comprising an increased amount of at least one polypeptidehaving a sequence selected from the group consisting of SEQ ID Nos. 1 to23, 47 to 52, and 64 to 65.

Embodiment 45. The cured tobacco leaf of any one of embodiments 39 to41, wherein said chorismate mutase-like polypeptide has at least 80%homology to a sequence selected from the group consisting of SEQ ID NOs:68 to 70.

Embodiment 46. The cured tobacco leaf of any one of embodiments 39 to41, wherein said chorismate mutase-like polypeptide comprises a sequenceselected from the group consisting of SEQ ID NOs: 68 to 70.

Embodiment 47. The cured tobacco leaf of any one of embodiments 39 to41, wherein said chorismate mutase-like polypeptide is encoded by apolynucleotide sequence having at least 80% homology to a sequenceselected from the group consisting of SEQ ID NOs: 71 to 73.

Embodiment 48. The cured tobacco leaf of any one of embodiments 39 to41, wherein said chorismate mutase-like polypeptide is encoded by apolynucleotide sequence selected from the group consisting of SEQ IDNOs: 71 to 73.

Embodiment 49. The cured tobacco leaf of any one of embodiments 39 to41, wherein the amount of said one or more TSNAs is reduced by at least50% compared to a cured tobacco leaf or a tobacco product from a controltobacco plant not comprising said transgene.

Embodiment 50. The cured tobacco leaf of any one of embodiments 39 to41, wherein said cured tobacco leaf comprises less than 2 ppm totalTSNAs.

Embodiment 51. The cured tobacco leaf of any one of embodiments 39 to41, wherein said cured tobacco leaf comprises between 2 and 0.05 ppmtotal TSNAs.

Embodiment 52. The cured tobacco leaf of any one of embodiments 39 to41, wherein said cured tobacco leaf comprises less than 0.08 ppm4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), wherein the levelof said total TSNAs is measured based on a freeze-dried cured leafsample using liquid chromatograph with tandem mass spectrometry(LC/MS/MS).

Embodiment 53. The cured tobacco leaf of any one of embodiments 39 to41, wherein said one or more tobacco-specific nitrosamines (TSNAs) areselected from the group consisting of N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) N′-nitrosoanabasine (NAB), and any combination thereof.

Embodiment 54. The cured tobacco leaf of any one of embodiments 39 to41, wherein said cured leaf of a tobacco plant is selected from thegroup consisting of air-cured Burley tobacco, air-cured dark tobacco,fire-cured dark tobacco, and Oriental tobacco.

Embodiment 55. The cured tobacco leaf of any one of embodiments 39 to41, wherein said tobacco plant is selected from the group consisting ofa flue-cured variety, a Burley variety, a Maryland variety, a darkvariety, and an Oriental variety.

Embodiment 56. The cured tobacco leaf of any one of embodiments 39 to41, wherein said cured tobacco leaf is from a tobacco plant selectedfrom the group consisting a BU 64 plant, a CC 101 plant, a CC 200 plant,a CC 13 plant, a CC 27 plant, a CC 33 plant, a CC 35 plant, a CC 37plant, a CC 65 plant, a CC 67 plant, a CC 301 plant, a CC 400 plant, aCC 500 plant, CC 600 plant, a CC 700 plant, a CC 800 plant, a CC 900plant, a CC 1063 plant, a Coker 176 plant, a Coker 319 plant, a Coker371 Gold plant, a Coker 48 plant, a CU 263 plant, a DF911 plant, aGalpao plant, a GL 26H plant, a GL 338 plant, a GL 350 plant, a GL 395plant, a GL 600 plant, a GL 737 plant, a GL 939 plant, a GL 973 plant, aGF 157 plant, a GF 318 plant, an RJR 901 plant, an HB 04P plant, a K 149plant, a K 326 plant, a K 346 plant, a K 358 plant, a K394 plant, a K399 plant, a K 730 plant, an NC 196 plant, an NC 37NF plant, an NC 471plant, an NC 55 plant, an NC 92 plant, an NC2326 plant, an NC 95 plant,an NC 925 plant, a PVH 1118 plant, a PVH 1452 plant, a PVH 2110 plant, aPVH 2254 plant, a PVH 2275 plant, a VA 116 plant, a VA 119 plant, a KDH959 plant, a KT 200 plant, a KT204LC plant, a KY 10 plant, a KY 14plant, a KY 160 plant, a KY 17 plant, a KY 171 plant, a KY 907 plant, aKY 907LC plant, a KTY14×L8 LC plant, a Little Crittenden plant, a McNair373 plant, a McNair 944 plant, a male sterile KY 14×L8 plant, a NarrowLeaf Madole plant, a MS KY171 plant, a Narrow Leaf Madole (phph) plant,a MS Narrow Leaf Madole plant, a MS TND950 plant, a PD 7302LC plant, aPD 7305LC plant, a PD 7309LC plant, a PD 7312LC plant, a PD 7318LCplant, a PD 7319LC plant, a MSTKS 2002 plant, a TKF 2002 plant, a TKF6400 plant, a TKF 4028 plant, a TKF 4024 plant, a KT206LC plant, aKT209LC plant, a KT210LC plant, a KT212LC plant, an NC 100 plant, an NC102 plant, an NC 2000 plant, an NC 291 plant, an NC 297 plant, an NC 299plant, an NC 3 plant, an NC 4 plant, an NC 5 plant, an NC 6 plant, anNC7 plant, an NC 606 plant, an NC 71 plant, an NC 72 plant, an NC 810plant, an NC BH 129 plant, an NC 2002 plant, a Neal Smith Madole plant,an OXFORD 207 plant, a ‘Perique’ plant, a PVH03 plant, a PVH09 plant, aPVH19 plant, a PVH50 plant, a PVH51 plant, an R 610 plant, an R 630plant, an R 7-11 plant, an R 7-12 plant, an RG 17 plant, an RG 81 plant,an RG H51 plant, an RGH 4 plant, an RGH 51 plant, an RS 1410 plant, aSpeight 168 plant, a Speight 172 plant, a Speight 179 plant, a Speight210 plant, a Speight 220 plant, a Speight 225 plant, a Speight 227plant, a Speight 234 plant, a Speight G-28 plant, a Speight G-70 plant,a Speight H-6 plant, a Speight H₂O plant, a Speight NF3 plant, a TI 1406plant, a TI 1269 plant, a TN 86 plant, a TN86LC plant, a TN 90 plant, aTN90LC plant, a TN 97 plant, a TN97LC plant, a TN D94 plant, a TN D950plant, a TR (Tom Rosson) Madole plant, a VA 309 plant, and a VA 359plant.

Embodiment 57. A tobacco product comprising the cured tobacco leaf ofany one of embodiments 39 to 41.

Embodiment 58. The tobacco product of embodiment 57, wherein saidtobacco product is selected from the group consisting of a cigarillo, anon-ventilated recess filter cigarette, a vented recess filtercigarette, a cigar, snuff, pipe tobacco, cigar tobacco, cigarettetobacco, chewing tobacco, leaf tobacco, hookah tobacco, shreddedtobacco, cut tobacco, loose leaf chewing tobacco, plug chewing tobacco,moist snuff, and nasal snuff.

Embodiment 59. A bale of the cured tobacco leaf of any one ofembodiments 39 to 41.

Embodiment 60. A container of tobacco product comprising the curedtobacco leaf of any one of embodiments 39 to 41.

Embodiment 61. The container of tobacco product of embodiment 60,wherein said contained is selected from the group consisting of a box, acan, a pack, a tin, and a pouch.

Embodiment 62. A population of the modified tobacco plants capable ofproducing the cured tobacco leaf of any one of embodiments 39 to 41.

Embodiment 63. The cured tobacco leaf of embodiment 41, wherein saidwherein said regulator of phenylalanine biosynthesis is a regulatorytranscription factor.

Embodiment 64. A method for reducing the amount of one or more TobaccoSpecific Nitrosamines (TSNAs) in a cured leaf of a tobacco plant, saidmethod comprising the steps of:

introducing a transgene encoding or targeting a phenylalaninebiosynthetic enzyme, a regulator of phenylalanine biosynthesis, or aphenylalanine metabolic enzyme; and

reducing the amount of said one or more TSNAs in a cured leaf of saidtobacco plant or a tobacco product made from said cured tobacco leaf.

Embodiment 65. A method for reducing the amount of one or more TSNAs ina cured leaf of a tobacco plant, said method comprising the steps of:

introducing a genetic modification in an endogenous gene, wherein saidendogenous gene encodes a phenylalanine biosynthetic enzyme, a regulatorof phenylalanine biosynthesis, or a phenylalanine metabolic enzyme; and

reducing the amount of said one or more TSNAs in a cured leaf of saidtobacco plant or a tobacco product made from said cured tobacco leaf.

Embodiment 66. The method of embodiment 64 or 65, wherein said methodfurther comprises reducing the amount of total alkaloids by at least 10%in a cured leaf compared to a cured tobacco leaf or a tobacco productfrom a control tobacco plant not comprising said modification.

Embodiment 67. The method of embodiment 64 or 65, wherein the amount ofsaid one or more TSNAs is reduced by at least 50% compared to a curedtobacco leaf or a tobacco product from a control tobacco plant notcomprising said transgene.

Embodiment 68. The method of embodiment 64 or 65, wherein said curedtobacco leaf comprises less than 2 ppm total TSNAs.

Embodiment 69. The method of embodiment 64 or 65, wherein said curedtobacco leaf comprises between 2 and 0.05 ppm total TSNAs.

Embodiment 70. The method of embodiment 64 or 65, wherein said curedtobacco leaf comprises less than 0.08 ppm4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), wherein the levelof said total TSNAs is measured based on a freeze-dried cured leafsample using liquid chromatograph with tandem mass spectrometry(LC/MS/MS).

Embodiment 71. The method of embodiment 64 or 65, wherein said one ormore tobacco-specific nitrosamines (TSNAs) are selected from the groupconsisting of N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) N′-nitrosoanabasine (NAB), and any combination thereof.

Embodiment 72. The method of embodiment 64 or 65, wherein the amount ofsaid one or more TSNAs is reduced by at least 50% compared to a curedtobacco leaf or a tobacco product from a control tobacco plant notcomprising said transgene.

Embodiment 73. The method of embodiment 64 or 65, wherein said regulatorof phenylalanine biosynthesis is a regulatory transcription factor.

Embodiment 74. The method of embodiment 64 or 65, wherein said curedleaf of a tobacco plant is selected from the group consisting ofair-cured Burley tobacco, air-cured dark tobacco, fire-cured darktobacco, and Oriental tobacco.

Embodiment 75. The method of embodiment 64 or 65, wherein said tobaccoplant is selected from the group consisting of a flue-cured variety, aBurley variety, a Maryland variety, a dark variety, and an Orientalvariety.

Embodiment 76. The method of embodiment 64 or 65, further comprisingincreasing the amount of one or more antioxidants in said cured leaf ofa tobacco plant.

Embodiment 77. The method of embodiment 76, wherein said one or moreantioxidants are selected from the group consisting of flavanone,flavanol, flavone, flavonol, isoflavone, hydroxybenzoic acid,hydroxycinnamic acid, ellagitannin, stibene, lignan, carotenoids, andglycyrrhzin.

Embodiment 78. The method of embodiment 76, wherein said one or moreantioxidants are selected from the group consisting of Naringenin,Catechin, Epicatechin, Apigenin, Luteonin, Quercetin, Myricetin, Rutin,Genistein, Daidzein, Gallic acid, Vanillic acid, Protocatechuic acid,Ferunic acid, Cinnamic acid, Coumeric acid, Chlorogenic acid, Coffeicacid, ferulic acid, Sanguiin, Resveratrol, Sesamin, Caretonoids, andVitamin C.

Embodiment 79. The method of embodiment 64, wherein said transgeneencodes a chorismate mutase-like polypeptide.

Embodiment 80. The method of embodiment 79, wherein said chorismatemutase-like polypeptide has at least 80% homology to a sequence selectedfrom the group consisting of SEQ ID NOs: 68 to 70.

Embodiment 81. The method of embodiment 79, wherein said chorismatemutase-like polypeptide comprises a sequence selected from the groupconsisting of SEQ ID NOs: 68 to 70.

Embodiment 82. The method of embodiment 79, wherein said chorismatemutase-like polypeptide is encoded by a polynucleotide sequence havingat least 80% homology to a sequence selected from the group consistingof SEQ ID NOs: 71 to 73.

Embodiment 83. The method of embodiment 79, wherein said chorismatemutase-like polypeptide is encoded by a polynucleotide sequence selectedfrom the group consisting of SEQ ID NOs: 71 to 73.

Embodiment 84. The method of embodiment 65, wherein said endogenous geneencodes a chorismate mutase-like polypeptide.

Embodiment 85. The method of embodiment 84, wherein said chorismatemutase-like polypeptide has at least 80% homology to a sequence selectedfrom the group consisting of SEQ ID NOs: 68 to 70.

Embodiment 86. The method of embodiment 84, wherein said chorismatemutase-like polypeptide comprises a sequence selected from the groupconsisting of SEQ ID NOs: 68 to 70.

Embodiment 87. The method of embodiment 84, wherein said chorismatemutase-like polypeptide is encoded by a polynucleotide sequence havingat least 80% homology to a sequence selected from the group consistingof SEQ ID NOs: 71 to 73.

Embodiment 88. The method of embodiment 84, wherein said chorismatemutase-like polypeptide is encoded by a polynucleotide sequence selectedfrom the group consisting of SEQ ID NOs: 71 to 73.

Embodiment 89. The method of embodiment 64 or 65, wherein said tobaccoplant further comprises a second transgene encoding or targeting anantioxidant biosynthetic enzyme, a regulatory transcription factor of anantioxidant, an antioxidant transporter, an antioxidant metabolicenzyme.

Embodiment 90. The method of embodiment 89, wherein said secondtransgene encodes or targets a biosynthetic enzyme, a regulatorytranscription factor, a transporter, a metabolic enzyme, or acombination thereof, for one or more antioxidants selected from thegroup consisting of flavanone, flavanol, flavone, flavonol, isoflavone,hydroxybenzoic acid, hydroxycinnamic acid, ellagitannin, stibene,lignan, carotenoids, and glycyrrhzin.

Embodiment 91. The method of embodiment 89, wherein said secondtransgene encodes or targets a biosynthetic enzyme, a regulatorytranscription factor, a transporter, a metabolic enzyme, or acombination thereof, for one or more antioxidants selected from thegroup consisting of Naringenin, Catechin, Epicatechin, Apigenin,Luteonin, Quercetin, Myricetin, Rutin, Genistein, Daidzein, Gallic acid,Vanillic acid, Protocatechuic acid, Ferunic acid, Cinnamic acid,Coumeric acid, Chlorogenic acid, Coffeic acid, ferulic acid, Sanguiin,Resveratrol, Sesamin, Caretonoids, and Vitamin C.

Embodiment 92. The method of embodiment 89, wherein said secondtransgene encodes a protein comprising a sequence having at least 80%identity to a sequence selected from the group consisting of SEQ ID NOs:1 to 23, 47 to 52, and 64 to 65.

Embodiment 93. The method of embodiment 65, wherein said endogenous geneencodes a protein comprising a sequence having at least 80% identity toa sequence selected from the group consisting of SEQ ID NOs: 1 to 23, 47to 52, and 64 to 65.

EXAMPLES Example 1. Plant Transformation

Tobacco plants overexpressing a gene of interest are generated viaAgrobacterium-mediated transformation. An expression vector, p45-2-7(FIG. 2 ), is used as a backbone to generate multiple transformationvectors. p45-2-7 contains a CsVMV promoter, a NOS terminator, and acassette comprising a kanamycin selection marker (NPT II) operablylinked to an Actin2 promoter and a NOS terminator. Nucleic acid vectorscomprising transgenes of interest are introduced into tobacco leaf discsvia Agrobacterium transformation. See, for example, Mayo et al., 2006,Nat Protoc. 1:1105-11 and Horsch et al., 1985, Science 227:1229-1231.

Narrow Leaf Madole (NLM) tobacco plants are grown in MagentaTM GA-7boxes and leaf discs are cut and placed into Petri plates. Agrobacteriumtumefaciens cells comprising a transformation vector are collected bycentrifuging a 20 mL cell suspension in a 50 mL centrifuge tube at 3500RPM for 10 minutes. The supernatant is removed and the Agrobacteriumtumefaciens cell pellet is re-suspended in 40 mL liquid re-suspensionmedium. Tobacco leaf, avoiding the midrib, are cut into eight 0.6 cmdiscs with a #15 razor blade and placed upside down in a Petri plate. Athin layer of Murashige & Skoog with B5 vitamins liquid re-suspensionmedium is added to the Petri plate and the leaf discs are pokeduniformly with a fine point needle. About 25 mL of the Agrobacteriumtumefaciens suspension is added to the Petri plate and the leaf discsare incubated in the suspension for 10 minutes.

Leaf discs are transferred to co-cultivation Petri plates (½ MS medium)and discs are placed upside down in contact with filter paper overlaidon the co-cultivation TOM medium (MS medium with 20 g/L sucrose; 1 mg/Lindole-3-acetic acid; and 2.5 mg/L 6-benzyl aminopurine (BAP)). ThePetri plate is sealed with parafilm prior to incubation in dim light(60-80 mE/ms) with 18 hours on, 6 hours off photoperiods at 24 degreesCelsius for three days. After incubation, leaf discs are transferred toregeneration/selection TOM K medium Petri plates (TOM medium plus 300mg/L kanamycin). Leaf discs are sub-cultured bi-weekly to fresh TOM Kmedium in dim light with 18 hours on, 6 hours off photoperiods at 24degrees Celsius until shoots become excisable. Shoots from leaf areremoved with forceps and inserted in MS basal medium with 100 mg/Lkanamycin. Shoots on MS basal medium with 100 mg/L kanamycin areincubated at 24 degrees Celsius with 18 hours on, 6 hours offphotoperiods with high intensity lighting (6080 mE/ms) to inducerooting.

When plantlets containing both shoots and roots grow large enough (e.g.,reach approximately half the height of a Magenta™ GA-7 box), they aretransferred to soil. Established seedlings are transferred to agreenhouse for further analysis and to set seed. Control plants areeither NLM plants that have not been transformed or NLM plants that havebeen transformed with an empty p45-2-7 vector.

Example 2. AtPAP1 Overexpressing Plants Comprise Reduced TSNAs

Tobacco plants overexpressing AtPAP1 are generated viaAgrobacterium-mediated transformation. AtPAP1, comprising SEQ ID NO:46,is incorporated into an overexpression vector and transformed intotobacco as described in Example 1. After transformation, establishedseedlings are transferred to a greenhouse for further analysis and toset seed. Transformed plants are developmentally similar to controlplants except that they exhibit a purple color due to anthocyaninaccumulation as shown in FIG. 3 . To determine TSNA amounts, tobaccoplants are grown under standard conditions and topped at flowering. Fourto six weeks after topping, plants are harvested and leaf is cured usingeither air or fire curing methods.

Leaves are cured using both air and fire curing methods. The standardfire curing method used in this study is based on the 2017-2018 Burleyand Dark Tobacco production guide (B. Pearce ed., (2017)). After thepre-curing methods described in Example 1 above, 15 sticks of tobaccofrom each of the five experimental varieties are placed in a barn. Eachexperimental barn is filled with all varieties at the same time. Thefirst phase is the yellowing phase. Tobacco is allowed to yellow and thefirst firing is performed when yellowing is nearly complete. The firstfiring is performed between five and eight days after housing and theinitial fires are about 100° F. Barn top ventilators are left openduring this phase.

The second phase is color setting. Color setting begins when yellowingis completed which is indicated by a solid yellow leaf lamina withlittle or no brown color. During color setting the temperature isincreased to between 37.7° C. and 46.1° C. (100° F. and 115° F.) withadditional fires. Barn top ventilators are closed during this phase.Color setting conditions are maintained until the leaf lamina is a solidbrown color. This phase lasts between 7 and 14 days and involvesmultiple firings. Ventilators are opened between firings. Brown colorappearing one-half to two-thirds up the leaf indicates the end of thecolor setting phase.

The third phase is drying. During drying, ventilators are opened andheat is increase to no greater than 54.4° C. (130° F.). Drying iscomplete when little to no green color is present and when the tobaccolamina shatters when touched.

The final phase is finishing phase. After drying, barn temperatures aremaintained at no greater than 48.9° C. (120° F.). The barn is ventilatedfor several days before two slow firings over a 10 to 14 day period toimpart a smoke finish. Smoke volume is maximized to impart smoke finishcharacteristics to the leaf surface. The firing phase uses little to noventilation.

The standard air curing method used in this study is based on the2017-2018 Burley and Dark Tobacco production guide (B. Pearce ed.,(2017)). After the pre-curing phase, 15 sticks of tobacco from each ofthe five experimental varieties are placed in a barn. Each experimentalbarn is filled with all varieties at the same time. Ventilators are usedto maintain adequate air flow and to modulate temperature and humidityinside the barn. When mean daytime temperatures are above 26.6° C. (80°F.) and mean nighttime temperatures are above 15.5° C. (60° F.) barndoors and ventilators are open during the yellowing and color settingstages. During cool temperature conditions (mean daytime temperaturebelow 18.3° C. (65° F.)), heat sources can be used to increase the barntemperature to no more than 32.2° C. (90° F.). At the end of theair-curing process, the tobacco is sampled for chemistry analysis.

The amounts of four TSNAs are measured: N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) and N′-nitrosoanabasine (NAB) are measured. Cured leaf samples arefreeze dried and crushed to 1 mm. For TSNA analysis, 750 mg of crushed,freeze-dried leaf is added to 30 mls of 10 mM ammonium acetate. Afterincubation in a shaker for 30 minutes, approximately 4 mls of sample istransferred into disposable culture tubes containing 0.25 ml ofconcentrated ammonium hydroxide. The sample is vortexed briefly and 1.5mls is added to a prewashed and conditioned extraction cartridge with aflow rate of 1 to 2 drops per second. Analytes are eluted from thesample using 1.5 mls of 70:30 methanol with 0.1% acetic acid. Samplesare analyzed using liquid chromatography with tandem mass spectrometry(LC/MS/MS).

The effect of AtPAP1 overexpression on TSNA levels is determined forfive T₁ AtPAP1 overexpression lines (six plants each) after cultivationin the greenhouse. Measurements of NNN, NNK, NAB, and NAT in T₀ AtPAP1overexpressing plants are shown in Table 1. Total TSNA levels areconsiderably reduced in AtPAP1 plants as shown in FIG. 4A. Considerablereductions in NNK levels (FIG. 4B), NNN levels (FIG. 4C), NAB levels(FIG. 4D), and NAT levels (FIG. 4E) are also observed.

The effect of AtPAP1 overexpression on TSNA levels is consistent insubsequent generations grown under field conditions. Total TSNA levels,as well as the levels of NNN, NNK, NAT, and NAB, are consistentlyreduced under both air and fire cured conditions for T₂. (See Table 2).

TABLE 1 TSNA levels in AtPAP1 overexpression plants are reduced comparedto controls. Total NNN NNK NAB NAT TSNA % TSNA Plant ID Variety (ppm)(ppm) (ppm) (ppm) (ppm) Reduction 12GH471 t-NL 0.087 0.035 0.008 0.0590.189 95.98 Madole LC T821 (PAP1 OEX) 12GH472 t-NL 0.091 0.031 0.0050.048 0.175 96.28 Madole LC T824 (PAP1 OEX) 12GH473 t-NL 0.105 0.0370.01 0.069 0.221 95.30 Madole LC T827 (PAP1 OEX) 12GH474 t-NL 0.1640.043 0.011 0.103 0.321 93.18 Madole LC T827 (PAP1 OEX) 12GH475 t-NL0.089 0.036 0.008 0.067 0.2 95.75 Madole LC T836 (PAP1 OEX) Control NL1.581 1.232 0.079 1.812 4.704 — Madole

TABLE 2 TSNA levels in AtPAP1 overexpressing plants grown in a field andair or fire cured. S5759 is a control line and TS3615 and TS3617 areindependently derived AtPAP1 overexpressing lines. NNN NNK NAB NAT TotalTSNA (ppm) (ppm) (ppm) (ppm) (ppm) Fire-Cured S5759 2.96 0.85 0.27 4.368.44 TS3615 0.66 0.29 0.06 0.82 1.83 TS3617 0.88 0.37 0.08 1.06 2.39Air-Cured S5759 0.62 0.08 0.03 0.68 1.41 TS3615 0.16 0.06 0.01 0.14 0.37TS3617 0.13 0.06 0.01 0.12 0.32

Example 3. AtPAP1 Overexpressing Plants Exhibit Increased Oxygen RadicalAbsorbance Capacity

The effect of AtPAP1 overexpression on oxidative capacity is determinedfor five T₁ AtPAP1 overexpression lines (six plants each) aftercultivation in the greenhouse. Oxygen Radical Absorbance Capacity (ORAC)is measured to determine antioxidant activity in AtPAP1 overexpressingplants. Quenching of a Progallol Red (PGR) florescent probe is used todetermine the ORAC measurement according to manufactures instruction(BioTek, Winooski, Vt.). Antioxidants are extracted from crushed tissuesamples with a methanol/HCL extraction buffer (6/1, v/v). The samplesare incubated for 30 minutes at 37° C. in a reaction mixture containing75 mM phosphate buffer, pH 7.4, and 5 μM PGR. After incubation, 37° C.AAPH solution is added to the reaction mixture to a final concentrationof 10 mM. Controls with all the solution components, but without thetissue samples, are used for comparison.

Reaction and control samples are shaken and the absorption (A) isrecorded every 30 seconds for 180 minutes. The kinetic values arerecorded as A/A_(time0). ORAC scores are determined based on the AreaUnder Curve (AUC) values determined scores from the sample and blank.ORAC scores are assessed for all time-points until the A/A_(time0)reaches a value of 0.2 using MicroCal Origin (R17.0, Boston, Mass.).ORAC values are recorded in FIG. 5 demonstrating increased ORAC valuesin AtPAP1 overexpression lines.

Example 4. Alkaloid Levels in Tobacco Plants Expressing AtPAP1

The effect of AtPAP1 overexpression on total alkaloid levels isdetermined for five T₁ AtPAP1 overexpression lines (six plants each)after cultivation in the greenhouse. The levels of the alkaloidsnicotine, nornicotine, anatabine, and anabasine are determined with GasChromatography followed by Mass Spectrometry (GC-MS). For example,measurement of anatabine is performed by mixing one gram of cured leaftissue with 10 mls of 2N NaOH, followed by incubation at roomtemperature for fifteen minutes. Anatabine is then extracted by additionof 50 mls of 0.04% quinolone (w/v) dissolved in methyl-tert-butyl etherfollowed by rotation on a linear shaker for three hours. After phaseseparation, alkaloid levels are determined using an Agilent 6890 GasChromatograph and an Agilent 5973N Mass Spectrometer. The results ofmeasurements for the alkaloids nicotine, nornicotine, anatabine, andanabasine are recorded in Table 3.

Alkaloid levels in field grown plants are also reduced after bothair-curing and fire-curing. Tobacco plants overexpressing AtPAP1 aregrown in a field, harvested, and both air and fire cured as described inExample 2. Total alkaloid levels are reduced under both air and firecuring conditions (See Table 4). The levels of nicotine, nornicotine,anatabine, and anabasine are also reduced under both air and fire curingconditions (See Table 4).

TABLE 3 Alkaloid levels in greenhouse grown AtPAPI overexpressing plantsare mildly reduced compared to controls. Nicotine Nornicotine AnabasineAnatabine Plant ID Variety (% by wt) (% by wt) (% by wt) (% by wt)12GH471 t-NL Madole LC 3.679 0.046 0.009 0.038 T821 (PAP1 OEX) 12GH472t-NL Madole LC 3.009 0.089 0.008 0.034 T824 (PAP1 OEX) 12GH473 t-NLMadole LC 4.323 0.073 0.011 0.048 T827 (PAP1 OEX) 12GH474 t-NL Madole LC4.609 0.052 0.009 0.037 T827 (PAP1 OEX) 12GH475 t-NL Madole LC 3.3290.036 0.008 0.034 T836 (PAP1 OEX) Control NL Madole 5.921 0.09  0.0140.074

TABLE 4 TSNA levels in AtPAP1 overexpressing plants grown in a field andair or fire cured S5759 is a control line and TS3615 and TS3617 areindependently derived AtPAP1 overexpressing lines. Nicotine NornicotineAnabasine Anatabine Total Alkaloids (%) (%) (%) (%) (%) Fire-Cured S57595.973 0.073 0.018 0.101 6.164 TS3615 4.215 0.037 0.01 0.049 4.311 TS36174.533 0.038 0.011 0.048 4.629 Air-Cured S5759 7.117 0.181 0.022 0.137.449 TS3615 5.217 0.078 0.013 0.062 5.369 TS3617 5.51 0.059 0.014 0.0635.646

Example 5. AtPAP1 Overexpressing Plants Comprise Reduced Nitrite

The effect of AtPAP1 overexpression on nitrite and nitrate levels isdetermined for five T₁ AtPAP1 overexpression lines (six plants each)after cultivation in the greenhouse. Cured leaf Samples are prepared asin Example 2 for LC/MS/MS and tested. Nitrite and nitrate levels asshown in FIG. 6A and FIG. 6B. The overexpression of AtPAP1 reduces thelevel of nitrite but not nitrate.

Example 6. Reduced Chlorogenic Acid in Tobacco Leaf Correlates withElevated TSNA Levels

The level of additional antioxidants are modulated to furtherdemonstrate a negative correlation between antioxidants and TSNAs.Reduction of Chlorogenic acid (CGA) levels results in an increase intotal TSNAs and total alkaloids. CGA or Caffeoyl quinate is generatedfrom Caffeoyl CoA or p-Coumaroyl CoA through the activity ofhydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase (HQT) andhydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase(HCT) (Payyavula et al., 2015, Plant Biotechnology Journal, Hoffmann etal., 2004, The Plant Cell, FIG. 7 ). The activity of these enzymes isreduced in tobacco by silencing HCT and HQT with RNAi. Silencing HQT andHCT results in a reduction of CGA as shown in FIG. 8 and an increase intotal TSNAs as shown in FIG. 9 .

Transformation vectors comprising RNAi constructs are designed toinhibit the expression of tobacco genes that promote the conversion ofCaffeoyl CoA or p-Coumaroyl CoA to CGA. Modified tobacco plants andcontrol tobacco plants are created and grown as described in Example 1.Cured leaf samples from the modified tobacco plants are prepared forevaluation of TSNAs, alkaloids, and nitrite/nitrate as described inExamples 2, 4 and 5. Alkaloid levels show mild modulations as shown inTable 5. A negative correlation is observed between CGA levels and TSNAlevels, as well as the levels of individual TSNAs (NNN, NNK, NAB, andNNA) as shown in FIG. 10A-E and Table 6. Nitrite levels are unchangedand nitrate levels show reductions compared to controls (Table 6).

TABLE 5 Alkaloid and CGA levels in HCT and HQT RNAi lines grown in agreenhouse. Nicotine Nornicotine Myosmine Anabasine Anatabine CGA (% bywt) (% by wt) (% by wt) (% by wt) (% by wt) (mg/g) K326 HQT-1 3.900.10775 0.007918 0.0217 0.109775 1.8525 K326 HQT-2 4.10 0.1122750.006815 0.022825 0.106125 2.07 K326 HQT-3 4.04 0.115 0.006995 0.0210250.103175 2.17 K326 HCT-1 3.59 0.095625 0.006978 0.018425 0.091025 7.6375K326 HCT-2 3.45 0.083525 0.005678 0.0178 0.085525 8.1075 K326 HQT-4 3.930.0972 0.00643 0.01985 0.10085 8.5025 K326 HCT-3 3.28 0.07795 0.0061980.0154 0.074925 9.65 K326 Control 3.45 0.09165 0.007213 0.0185750.094975 8.775

TABLE 6 TSNA, CGA, Nitrite and Nitrate levels in HQT and HCT RNAi plantsgrown in a greenhouse. LL LL LL LL LL LL LL NNN NNK NAB NAT TSNA NitriteNitrate CGA (ppm) (ppm) (ppm) (ppm) (ppm) (ppm) (ppm) (mg/g) K326 HQT-10.205 0.08425 0.02675 0.2875 0.6035 0.245 3192.5 1.8525 K326 HQT-20.2175 0.09825 0.0285 0.2925 0.63675 0.2 3257.5 2.07 K326 HQT-3 0.1950.1265 0.02475 0.265 0.61125 0.22 2685 2.17 K326 HCT-1 0.13325 0.06350.02 0.165 0.38175 0.2 3285 7.6375 K326 HCT-2 0.0955 0.07025 0.020.13075 0.3165 0.2225 3202.5 8.1075 K326 HQT-4 0.11475 0.07 0.0215 0.1550.36125 0.215 2655 8.5025 K326 HCT-3 0.088 0.0635 0.02 0.1085 0.280.2525 2945.5 9.65 K326 Control 0.0885 0.0575 0.02 0.1165 0.2825 0.21862.5 8.775

Example 7: Increased Antioxidant Capacity in Field Grown AtPAP1Overexpressing Plants

A Ferric Reducing Antioxidant Power (FRAP) analysis is conducted onfield grown tobacco plants overexpressing AtPAP1. AtPAP1 overexpressionconstructs are transformed into TN90 and Narrow Leaf Madole (NLM)tobacco plants as described in Example 1. Modified and unmodifiedcontrol plants are grown in a field under standard field conditions.Plants are topped at flowering and leaves for analysis are collectedharvest stage (4 weeks) later. At least five plants from two independenttransgenic events in both the TN90 background and the NLM background andat least five plants from unmodified TN90 and NLM plants are sampled andtested. 10 mg of freeze dried leaf is taken into an Eppendorf tube and1500 μl of 80% ethanol is added and sonicated for 10 minutes. Aftercentrifuge, 5-10 μl of supernatant is used to measure antioxidantcapacity.

The Ferric Reducing Antioxidant Power (FRAP) method is based on thereduction of complexes of 2,4,6-tripyridyl-s-triazine (TPTZ) with ferricchloride hexahydrate (FeCl3.6H20) which forms blue ferrous complexesafter its reduction (Benzie & Strain, 1996, Analytical Biochemistry,239, 70-76). Three solutions are used for the assay: Solution 1) 10mmol·L-1 solution of TPTZ (0.07802 g/25 mL), in 40 mM of hydrochloricacid; Solution 2) 20 mM solution of ferric chloride hexahydrate (0.13513g/25 mL) in ACS water; Solution 3) 20 mM acetate buffer, pH 3.6 (weightof sodium acetate trihydrate is 0.27216 g in 100 mL ACS water, adjustedto the desired pH using HCl). These three solutions (TPTZ, FeCl3,acetate buffer) are mixed in a 1:1:10 ratio. A 245 μL volume of themixed solution is pipetted into a plastic cuvette with subsequentaddition of a 5 μL sample (gallic acid, Trolox®). Absorbance is measuredat primary λ 593 nm wavelength. Different concentrations of Trolox® wasused to make a standard curve and samples are compared to standardcurve. Total antioxidants are calculated using the following equation

${{Antioxidants}\left( {n{mol}/{mg}} \right)} = \frac{\begin{matrix}{n{moles}{present}{in}{the}{sample} \times} \\{{total}{sample}{extraction}{volume}}\end{matrix}}{\begin{matrix}{{total}{wt}{of}{the}{sample} \times} \\{{volume}{used}{for}{measurement}}\end{matrix}}$

Modified tobacco plants overexpressing AtPAP1 show a significantlyincreased antioxidant capacity as measured by FRAP analysis compared tothe unmodified controls (P<0.01) (FIG. 13 ).

Example 8. Secondary Metabolite Accumulation in Field Grown AtPAP1Overexpressing Plants

A secondary metabolite accumulation analysis is conducted on field grownAtPAP1 overexpressing plants. AtPAP1 overexpression constructs aretransformed into Narrow Leaf Madole (NLM) tobacco plants as described inExample 1. Modified and unmodified control plants are grown in a fieldunder standard conditions. Plants are topped at flowering and leaves foranalysis are collected two weeks later from two independently modifiedNLM plants (D1 and D2) and one unmodified NLM plant. A set ofBenzenoids, Flavonoids, and Phenylpropanoids show significantlyincreased levels in modified plants compared to unmodified plants(P<0.01) (See Table 7).

The levels of the alkaloids nicotine, nornicotine, anatabine, andanabasine are determined with Gas Chromatography followed by MassSpectrometry (GC-MS). For example, measurement of anatabine is performedby mixing one gram of cured leaf tissue with 10 mls of 2N NaOH, followedby incubation at room temperature for fifteen minutes. Anatabine is thenextracted by addition of 50 mls of 0.04% quinolone (w/v) dissolved inmethyl-tert-butyl ether followed by rotation on a linear shaker forthree hours. After phase separation, alkaloid levels are determinedusing an Agilent 6890 Gas Chromatograph and an Agilent 5973N MassSpectrometer.

TABLE 7 Secondary metabolite accumulation in 35:AtPAP1 overexpressingNarrow Leaf Madole tobacco plants. Transgene Effects Transgene Effects(FLOWERING) Transgene Effects (HARVEST) (CURED) NP1_F/ NP2_F/ TP1_F/TP2_F/ NP1_H/ NP2_H/ TP1_H/ TP2_H/ NP1_C/ NP2_C/ Sub Pathway BiochemicalName NLMC_F NLMC_F TNC_F TNC_F NLMC_H NLMC_H TNC_H TNC_H NLMC_C NLMC_CAlkaloids cotinine 0.38 0.51 0.41 0.64 0.47 0.32 0.41 0.35 0.76 0.72nornicotine 0.44 0.52 0.54 0.81 0.55 0.49 0.62 0.49 0.57 0.58 anatabine0.67 0.69 0.65 0.82 0.62 0.52 0.71 0.56 0.69 0.63 nicotine 0.57 0.64 0.81.12 0.82 0.74 0.88 0.75 0.81 0.83 norcotinine 0.09 0.26 0.1 0.2 0.390.34 0.44 0.25 0.49 0.5 Benzenoids 4-hydroxybenzoate 5.33 4.8 3.52 2.913.25 2.85 6.87 7.37 1.95 1.9 protocatechuic acid- 7.99 7.52 10.01 8.445.08 4.09 7.5 6.99 1 1 3-glucoside Flavonoids dihydrokaempferol 4.487.74 16.46 7.73 13.57 15.88 22.2 14.24 8.64 11.66 dihydroquercetin 2.81.35 1.13 1 1 15.84 2.38 9.99 1.41 1 naringenin 4.55 5.71 3.52 2.37 3.273.48 2.84 2.78 4.67 8.62 naringenin 7-O- 7.03 9.54 24.63 16.99 4.3 8.955.13 5.09 1 1 glucoside quercetin 3- 1.44 1.52 1.64 2.19 0.73 51.7 3.9319.21 8.46 8.43 galactoside rutin (quercetin 3- 0.76 0.71 1.11 1.6 0.454.22 1.11 4.21 3.08 4.58 rutinoside) 3-methoxyapigenin 1.04 1 0.49 0.670.69 0.69 0.52 1.03 1.12 0.93 kaempferol 3-O- 0.42 0.47 0.88 0.97 0.440.97 0.87 0.86 3.02 3.6 glucoside/galactoside rutinose 44.98 36.54101.69 81.72 21.31 21.37 47.26 50.06 3.31 2.94 Phenylpropanoidschlorogenate 2.1 2.01 2.25 2.13 2.63 47.37 1.33 8.85 3.61 5.354-hydroxycinnamate 2.03 2.13 5.11 2.55 5.85 4.17 5.2 5.04 3.21 3.31ferulate 2.28 4.44 2.31 2.11 1.6 1.13 1.13 1.04 1.38 1.4 sinapoylaldehyde 2.03 2.38 2.25 1.55 2.04 2.27 2.77 2.39 1.17 0.96dihydroferulic acid 2.61 3.58 4.61 5.16 3.37 2.52 3.72 3.76 1.04 1.03coumaroylquinate 1.99 1.88 5.17 4.2 6.75 8.6 9.49 9.97 9.23 13.81 (2)coumaroylquinate 3.71 3.28 7.38 5.59 8.46 10.56 7.56 8.59 4.44 7.28 (4)coumaroylquinate 1.41 1.22 5.03 4.11 3.24 4.04 8.14 9.35 4.5 7.37 (5)coumaroylquinate 0.99 0.92 2.95 2.62 1.84 2.15 3.58 4.39 2.88 4.82 (3)NP1_F represents NLMPAP_TS3615 at flowering time; NP2_F representsNLMPAP_TS3617 at flowering time; NP1_H represents NLMPAP_TS3615 atharvest time; NP2_H represents NLMPAP_TS3617 at harvest time; NLMCFrepresents NL Madole Control at flowering time; NLMC_H represents NLMadole Control at harvest time; TP1_F represents TN90PAP_TS3613 atflowering time; TP2_F represents NLMPAP_TS3644 at flowering time; TP1_Frepresents TN90PAP_TS3613 at harvest time; TP2_F representsNLMPAP_TS3644 at harvest time; TNC_F represents TN90 Control atflowering time; and TNC_H represents TN90 Control at harvest time.

Example 9. Expression of Additional Genes to Modulate TSNA Levels

Transformation vectors and modified tobacco plants are generated tooverexpress full-length coding sequences from tobacco genes (e.g., SEQID NOs: 24-42, 44, 45, 53 to 58, 66 to 67, and 71 to 73) or non-tobaccoorigin genes (e.g., SEQ ID NOs: 43 and 46) that promote or are involvedin the production or accumulation of one or more antioxidants (See Table8). The overexpression of transcription factors that promote or areinvolved in the production or accumulation of one or more antioxidantsis described below.

NtAN2, SEQ ID NO: 30, is incorporated into a p45-2-7 transformationvector, and modified tobacco plants are generated, according toExample 1. Modified NLM tobacco plants (T₀ and T₁ generation) andcontrol tobacco plants are grown for 4-6 weeks after transplantation tosoil, harvested, and cured in PGC chambers. Cured leaf samples areprepared for evaluation of TSNAs, oxidative degradation potential,alkaloids, and nitrites/nitrates as described in Examples 2 to 5. A FRAPassay is used to determine antioxidant capacity in T₀ plants asdescribed in Example 7. Increased antioxidant capacity is detected inindividual field grown T₀ plants compared to the average antioxidantcapacity determined for at least five unmodified Narrow leaf Madoleplants (FIG. 14 ).

NtAN1a, SEQ ID NO: 28, is incorporated into a p45-2-7 transformationvector, and modified tobacco plants are generated, according toExample 1. Modified NLM tobacco plants (T₀ and T₁ generation) andcontrol tobacco plants are grown for 4-6 weeks after transplantation tosoil, harvested, and cured in PGC chambers. Cured leaf samples areprepared for evaluation of TSNAs, oxidative degradation potential,alkaloids, and nitrites/nitrates as described in Examples 2 to 5. A FRAPassay is used to determine antioxidant capacity in T₀ plants asdescribed in Example 7. Increased antioxidant capacity is detected inindividual greenhouse grown T₀ plants compared to the averageantioxidant capacity determined for at least five unmodified Narrow leafMadole plants (FIG. 15 ).

NtDFR, SEQ ID NO: 37, is incorporated into a p45-2-7 transformationvector, and modified tobacco plants are generated, according toExample 1. Modified NLM tobacco plants (T₀ and T₁ generation) andcontrol tobacco plants are grown for 4-6 weeks after transplantation tosoil, harvested, and cured in PGC chambers. Cured leaf samples areprepared for evaluation of TSNAs, oxidative degradation potential,alkaloids, and nitrites/nitrates as described in Examples 2 to 5. A FRAPassay is used to determine antioxidant capacity in T₀ plants asdescribed in Example 7. Increased antioxidant capacity is detected inindividual greenhouse grown T₀ plants compared to the averageantioxidant capacity determined for at least five unmodified Narrow leafMadole plants (FIG. 16 ).

NtJAF13, SEQ ID NO: 33, is incorporated into a p45-2-7 transformationvector, and modified tobacco plants are generated, according toExample 1. Modified NLM tobacco plants (T₀ and T₁ generation) andcontrol tobacco plants are grown for 4-6 weeks after transplantation tosoil, harvested, and cured in PGC chambers. Cured leaf samples areprepared for evaluation of TSNAs, oxidative degradation potential,alkaloids, and nitrites/nitrates as described in Examples 2 to 5. A FRAPassay is used to determine antioxidant capacity in T₀ plants asdescribed in Example 7. Increased antioxidant capacity is detected inindividual greenhouse grown T₀ plants compared to the averageantioxidant capacity determined for at least five unmodified Narrow leafMadole plants (FIG. 17 ).

NtMYB3, SEQ ID NO: 13, is incorporated into a p45-2-7 transformationvector, and modified tobacco plants are generated, according toExample 1. Modified tobacco plants (T₀ and T₁ generation) and controltobacco plants are grown for 4-6 weeks after transplantation to soil,harvested, and cured in PGC chambers. Cured leaf samples are preparedfor evaluation of TSNAs, oxidative degradation potential, alkaloids, andnitrites/nitrates as described in Examples 2 to 5. A FRAP assay is usedto determine antioxidant capacity in T₀ plants as described in Example7. Increased antioxidant capacity is detected in individual greenhousegrown T₀ plants compared to the average antioxidant capacity determinedfor at least five unmodified Narrow leaf Madole plants (FIG. 18 ).Plants overexpressing NtMYB3 show a normal leaf color in the T₀generation (FIG. 19 ). NtMYB3-like 1, 2, and 3, SEQ ID Nos: 64 to 65 arealso incorporated into a p45-2-7 transformation vector, and modifiedtobacco plants are generated, according to Example 1. Increasedantioxidant capacity is detected in plants overexpressing eitherNtMYB3-like 1, 2, or 3.

Chorismate mutase-like 1, 2a, and 2b, SEQ ID NOs: 68 to 70, areincorporated into a p45-2-7 transformation vector, and modified tobaccoplants are generated, according to Example 1. Modified NLM tobaccoplants (T₀ and T₁ generation) and control tobacco plants are grown for4-6 weeks after transplantation to soil, harvested, and cured in PGCchambers. Cured leaf samples are prepared for evaluation of TSNAs,oxidative degradation potential, alkaloids, and nitrites/nitrates asdescribed in Examples 2 to 5. A FRAP assay is used to determineantioxidant capacity in T₀ plants as described in Example 7. Increasedantioxidant capacity is detected in individual greenhouse grown T₀plants compared to the average antioxidant capacity determined for atleast five unmodified Narrow leaf Madole plants (FIG. 17 ).

TABLE 8 Nucleotide and protein sequences. Protein Coding Target SEQ IDSEQ ID Antioxidant Gene Function annotation Source No. No. AnthocyaninPutative alcohol tobacco  1 24 dehydrogenase; [Solanumlycopersicum(Tomato) (Lycopersicon esculentum).] Anthocyanin 1-O-acylglucose:tobacco  2 25 anthocyanin- O-acyltransferase; [Clitoria ternatea(Butterfly pea).] Chlorogenic 4-coumarate:CoA ligase; tobacco  3 26 acid[Ipomoea batatas (Sweet potato) (Convolvulus batatas).]. Also called 4CLChlorogenic 4-coumarate: tobacco  4 27 acid CoA ligase-like; [Nicotianasylvestris (Wood tobacco) (South American tobacco).]. Also called 4CL.Anthocyanin Anthocyanin 1a; tobacco  5 28 [Nicotiana tabacum (Commontobacco).]. Also called AN1a. Anthocyanin Anthocyanin 1b; tobacco  6 29[Nicotiana tabacum (Common tobacco).]. Also called AN1b. AnthocyaninAnthocyanin 2; tobacco  7 30 [Nicotiana tomentosiformis (Tobacco).]Anthocyanin anthocyanidin synthase tobacco  8 31 2 [Nicotiana tabacum].Also called ANS2. Anthocyanin leucoanthocyanidin tobacco  9 32dioxygenase [Nicotiana tabacum] Anthocyanin BHLH transcription tobacco10 33 factor JAF13; [Petunia hybrida (Petunia).] Ferulic acid Nicotianatabacum tobacco 11 34 caffeic acid O-methyltransferase II genechlorogenic trans-cinnamate 4- tobacco 12 35 acid monooxygenase-like[Nicotiana tomentosiformis], Also called C4H. Anthocyanin transcriptionfactor tobacco 13 36 MYB3-like [Nicotiana tabacum]; tobacco homolog ofAtPAP1 Anthocyanin Nicotiana tabacum tobacco 14 37 dihydroflavonol-4-reductase (LOC107797232) Anthocyanin Nicotiana tabacum tobacco 15 38NtDFR2 gene for dihydroflavonol- 4-reductase Anthocyanin Nicotianatabacum myb- tobacco 16 39 related protein 308-like (LOC107782378),mRNA-XM_016603259. Chlorogenic Nicotiana tabacum tobacco 17 40 acidshikimate O-hydroxy cinnamoyltransferase- like; also called HCT.Chlorogenic Nicotiana tabacum mRNA tobacco 18 41 acid forhydroxycinnamoyl CoA quinate transferase (hqt gene); also called HQT.Anthocyanin, Nicotiana tobacco 19 42 CGA, ferulic tabacum phenylalanineacid, ammonia lyase (tpa1) cinnamate, gene; also called PAL. coumaratecaffeic acid Anthocyanin Arabidopsis thaliana Arabidopsis 20 43 ttg1gene; WD40. carotenoids phytoene synthase 1 tobacco 21 44 [Nicotianatabacum] carotenoids phytoene synthase tobacco 22 45 2, chloroplastic[Nicotiana sylvestris] Anthocyanin Production of anthocyanin Arabidopsis23 46 pigment 1; PAPI. Flavonoids Phenylalanine ammonia- tobacco 47 53and lyase 4 (NtPAL4) anthocyanins Flavonoids Phenylalanine ammonia-tobacco 48 54 and lyase 2 (NtPAL2) anthocyanins Flavonoids Chaiconesynthase tobacco 49 55 and (NtCHS) anthocyanins Flavonoids Flavonol3-hydratase tobacco 50 56 and (NtF3H) anthocyanins Arogenatedehydrogenase tobacco 51 57 1 (NtADT1) Chlorogenic Arogenatedehydrogenase tobacco 52 58 acid, 2 (NtADT2) Flavonoids and anthocyaninsAnthocyanin transcription factor Myb3- tobacco 64 66 like 2 [Nicotianatabacum] Anthocyanin transcription factor Myb3- tobacco 65 67 like 3[Nicotiana tabacum] Chorismate mutase-like 1 tobacco 68 71 Chorismatemutase-like 2a tobacco 69 72 Chorismate mutase-like 2b tobacco 70 73

Example 10. Secondary Metabolite Accumulation in Greenhouse GrownTobacco Plants Overexpressing NtMYB3

A secondary metabolite accumulation analysis is conducted on greenhousegrown NtMYB3 overexpressing plants. NtMYB3 overexpression constructs arecreated as described in Example 9 and transformed into Narrow LeafMadole (NLM) tobacco plants as described in Example 1. Modified andunmodified control plants are grown in a greenhouse under standardconditions. Plants are topped at flowering and leaves for analysis arecollected two weeks later from two independently modified NLM plants (D1and D2) and one unmodified NLM plant. A set of Benzenoids, Flavonoids,and Phenylpropanoids show significantly increased levels in modifiedplants compared to unmodified plants (P<0.01) (See Table 9). The levelsof the alkaloids nicotine, nornicotine, anatabine, and anabasine aredetermined with Gas Chromatography followed by Mass Spectrometry (GC-MS)as described in Example 8.

Example 11. TSNA and Alkaloid Accumulation in Field Grown Tobacco PlantsOverexpressing AtPAP1 or NtMYB3

A TSNA and alkaloid accumulation analysis is conducted on field grownAtPAP1 and NtMYB3 overexpressing plants. AtPAP1 and NtMYB3overexpression constructs are created as described in Examples 2 and 9and transformed into Narrow Leaf Madole (NLM) dark tobacco plants asdescribed in Example 1. The AtPAP1 and NtMYB3 overexpression constructsare transformed into both NLM LC and NLM SRC plants. The accumulation inNLM LC is set to 100% as the control. Modified and unmodified controlplants are also grown under the same conditions. Plants are topped atflowering and leaves for analysis are collected two weeks later. Eachsample for analysis comprises 15 leaves with each leaf representing anindividual plant. The levels of the alkaloids nicotine, nornicotine,anatabine, and anabasine are determined as described in Example 8. TSNAsare measured as described in Example 2.

Overexpression of AtPAP1 or NtMYB3 significantly reduces both totalalkaloids and total TSNAs in dark tobacco. The reductions are seen indark tobacco leaves from plants that are grown in the field under bothfire and air curing. See FIGS. 22, 27, and 28 . The total reduction inTSNAs in these plants is the result of significant reductions in NNN,NNK, NAT, and NAB. Reductions in the individual TSNAs are in seen inboth fire cured leaves (See FIGS. 23 and 24 ) and air cured leaves (SeeFIGS. 25 and 26 ).

TABLE 9 Secondary metabolite accumulation in CsVMV:NtMYB3 overexpressingNarrow Leaf Madole tobacco plants. MYB3/ NLM NLM Metabolism BiochemicalName MYB3 Control Control Benzenoids benzoate 0.9089 0.2659  3.424-hydroxybenzoate 0.7365 0.4679  1.57 Phenylpropanoids chlorogenate5.9168 1.8605  3.18 aesculetin 1.5639 0.6389  2.45 sinapoyl aldehyde2.1063 0.8820  2.39 4-hydroxy cinnamate 0.4746 0.2061 2.3 lariciresinol1.0498 0.5342  1.97 cryptochlorogenic acid 2.6443 1.4087  1.88Terpenoids beta-cryptoxanthin 2.2629 1.0407  2.17 Aromatic aminotyrosine 2.2223 0.8026  2.77 acid metabolism tryptophan 1.6922 0.6446 2.63 (PEP derived) N-acetyltyrosine 0.6238 0.3467 1.83-dehydroshikimate 1.3611 0.7780  1.75 phenylalanine 1.0571 0.6024  1.75O-sulfo-L-tyrosine 0.4245 0.2499 1.7 Glutathione gamma- 0.7981 0.3127 2.55 metabolism glutamyltryptophan gamma- 1.5538 0.7072  2.2glutamylserine gamma- 0.2714 0.1436  1.89 glutamylglutamine glutathione,1.0281 0.5567  1.85 oxidized (GSSG) cysteine- 0.6539 0.3686  1.77glutathione disulfide gamma- 0.5800 0.3423  1.69 glutamylisoleucine*gamma-glutamylglycine 1.4032 0.9418  1.49

TABLE 10 A list of plant-origin antioxidants that can be used to reduceTSNAs. Chemical Classes Compounds Source of the Species AnthocyanidinDelphnidin Tobacco, Arabidopsis. Cabbage, potato or petunia CyanidinTobacco, Arabidopsis. Cabbage, potato or petunia Procyanidin Tobacco,Arabidopsis. Cabbage, potato or petunia Prodelphinidin Tobacco,Arabidopsis. Cabbage, potato or petunia Perlargonidin Tobacco,Arabidopsis. Cabbage, potato or petunia Peonidin Tobacco, Arabidopsis.Cabbage, potato or petunia Petunidin Tobacco, Arabidopsis. Cabbage,potato or petunia Flavanone Hesperetin Citrus or related speciesNaringenin Citrus or related species Flavanol Catechin Tobacco or otherrelated species Epicatechin Tobacco or other related species FlavoneApigenin Parsley, tobacco or other related species Luteonin Parsley,tobacco or other related species Flavonol Quercetin Red kidney bean orother related species Myricetin Red kidney bean or other related speciesRutin Tobacco, Red kidney bean or other related species IsoflavoneGenistein Soybean or other related species Daidzein Soybean or otherrelated species Hydroxybenzoic Gallic acid Tobacco, oak or Acid otherrelated species Vanillic acid Tobacco, Acai or other related speciesProtocatechuic Tobacco, Hibiscus or acid other related speciesHydroxycinnamic Ferunic acid Tobacco or other related species acidCinnamic acid Tobacco or other related species Coumeric acid Tobacco orother related species Chlorogenic acid Tobacco or other related speciesCoffeic acid Tobacco or other related species Ferulic acid Tobacco orother related species Ellagitannin Sanguiin Raspberry or other relatedspecies Chemical Classes Compounds Source of the Species StibeneResveratrol Grape or other related species Lignan Sesamin Sesame orother related species carotenoids Caretonoids Tobacco or carrots VitaminC Tobacco or carrots Glycyrrhzin Licorice

Example 12: Creation of Cisgenic Constructs to Modulate TSNA Levels

Cisgenic constructs are created to constitutively express AtPAP1, NtAN2,and NtAN1a. Tobacco native Ubiquitin (Ubi-4) or Tubulin (Tub) promotersare used in conjunction with a tobacco native heat shock protein (HSP)terminator. Sequences are incorporated into a p45-2-7 transformationvector, and modified tobacco plants are generated, according toExample 1. Constructs encoding Ubi4-P:PAP1-HSP-T (SEQ ID NO: 59),Ubi4-P:NtAN2-HSP-T (SEQ ID NO: 60), Tub-P:NtAN2-HSP-T (SEQ ID NO: 61),Ubi4-P:NtAN2-HSP-T:Tub-P:NtAN2-HSP-T (SEQ ID NO: 62), andUbi4-P:NtAN1a-HSP-T:Tub-P:NtAN2-HSP-T (SEQ ID NO: 63) are transformedinto tobacco plants. The presence of the cisgenic construct in atransformed plant is confirmed using amplicon sequencing. Modifiedtobacco plants (T₀ and T₁ generation) and control tobacco plants aregrown for 4-6 weeks after transplantation to soil, harvested, and curedin PGC chambers. Cured leaf samples are prepared for evaluation ofTSNAs, oxidative degradation potential, alkaloids, and nitrites/nitratesas described in Examples 2 to 7.

Example 13: Antioxidant Capacity of Phenylalanine Fed AtPAP1Overexpressing Plants

Plants overexpressing AtPAP1 are grown in a greenhouse to test theeffects of adding exogenous phenylalanine on antioxidant capacity. T₂AtPAP1 overexpression lines TS3615 and TS3617 along with control NLM aresterilized and grown on MS medium agar plates containing 0 mM (control),2 mM, and 4 mM phenylalanine. 25 plants per plate and 4 plates(replicates) per treatment are grown for 4 weeks under normal tissueculture conditions. After four weeks, all pooled leaf samples from aplate are harvested and tested for antioxidant capacity using a FRAPanalysis as described in Example 7. Leaves from plants treated with both2 mM and 4 mM phenylalanine showed increased FRAP activity compared toplants treated with the 0 mM control medium. Increase in FRAP activityis seen in both NLM as well as AtPAP1 overexpression lines TS3615 andTS3617 (See FIG. 21 ).

Example 14: Overexpression of Chorismate Mutase Increases Phenylalanine

Chorismate Mutase-like1, 2a, and 2b, having sequences of SEQ ID NOs: 68to 70 respectively, are incorporated into a p45-2-7 transformationvector, and modified tobacco plants are generated, according toExample 1. Modified NLM tobacco plants (T₀ and T₁ generation) andcontrol tobacco plants are grown for 4-6 weeks after transplantation tosoil, harvested, and cured in PGC chambers. Cured leaf samples areprepared for evaluation of TSNAs, oxidative degradation potential,alkaloids, and nitrites/nitrates as described in Examples 2 to 7. A FRAPassay is used to determine antioxidant capacity in T₀ plants asdescribed in Example 7. Increased antioxidant capacity is detected inindividual greenhouse grown T₀ plants compared to the averageantioxidant capacity determined for at least five unmodified Narrow leafMadole plants. T₀ plants overexpressing NtCM-like1, 2a, and 2b andhaving increased antioxidant capacity are identified and seed iscollected from these plants. T₁ seed is grown in a greenhouse to measurephenylalanine content after confirming Chorismate Mutase overexpression.Compared to control NLM plants, plants overexpressing NtCM-like1, 2a,and 2b have increased amounts of phenylalanine.

Example 15: Overexpression of Chorismate Mutase Increases AntioxidantCapacity

Plants overexpressing NtCM-like1, 2a, and 2b are created as described inExamples 1 and 9. The presence of overexpression constructs in atransformed plant is confirmed using amplicon sequencing. Plantsoverexpressing NtCM-like1, 2a, or 2b are grown in a greenhouse. Leavesamples are collected to measure antioxidant capacity using the FRAPassay as described in Example 7. Compared to control NLM plants, plantsoverexpressing NtCM-like1, 2a, and 2b have an increased antioxidantcapacity as measured using the FRAP assay.

Example 16: Overexpression of Chorismate Mutase Reduces TSNAs

Plants overexpressing NtCM-like1, 2a, and 2b are created as described inExamples 1 and 9 and grown in a greenhouse. The presence ofoverexpression constructs in a transformed plant is confirmed usingamplicon sequencing. Plants overexpressing NtCM-like1, 2a, or 2b aregrown in a greenhouse. Modified and control NLM tobacco is topped andleaves are harvested two weeks after topping. Leaves are cured usingeither air curing or fire curing methods as described in Example 2. Airand fire cured leaves are tested for TSNAs as described in Example 2.Plants overexpressing NtCM-like1, 2a, or 2b demonstrate reduced amountsof TSNAs compared to the unmodified NLM control plants.

Example 17: A Combination Approach for Further Reduction of TSNAs

A combination strategy is taken to combine Chorismate Mutaseoverexpression and the approach provided in Examples 2 to 7 to achieve afurther TSNA reduction. Plants are transformed with one or moreconstructs described in Example 9 and one or more of the constructsdescribed in Example 12 to achieve a further TSNA reduction. Antioxidantcapacity is measured as described in Example 9 and TSNAs levels aremeasured as described in Example 2. The modified plants having twotransgenes have TSNA amounts reduced more than modified tobacco plantshaving any one of the transgenes. Alternatively, a plant harboring oneor more transgenes described in Example 9 are crossed with a plantharboring one or more transgenes described in Example 13. F₁ plants aretested to insure the presence of each desired transgenes. F₁ plantscomprising one or more transgenes described in Example 9 and one or moretransgenes described in Example 13 have TSNA amounts reduced more thaneither of the parent plants.

Three nicotine demethylase genes, known as CYP82E4, CYP82E5, andCYP82E10, mediate nornicotine biosynthesis in Nicotiana tabacum. Tripleknockout mutants (cyp82e4, cyp82e5, cyp82e10) exhibit a dramaticreduction of nornicotine and consequently a reduction of NNN. Acombination strategy is taken to combine nicotine demethylase mutantsand the approach provided in Examples 2 to 7 to achieve a further TSNAreduction. A cyp82e4, cyp82e5, cyp82e10 triple mutant is transformedwith one or more constructs described in Example 9 to increaseantioxidant levels. Alternatively, cyp82e4, cyp82e5, cyp82e10 triplemutants are crossed with mutant or transgenic tobacco having elevatedantioxidant levels described in Example 2.

1-21. (canceled)
 22. A cured tobacco leaf of a modified tobacco plant,wherein said cured tobacco leaf comprises a decreased amount of one ormore tobacco specific nitrosamines (TSNAs), a recombinant nucleic acidmolecule comprising a promoter operably linked to a first polynucleotideencoding a Chorismate Mutase-like polypeptide having at least 95%sequence identity to a sequence selected from the group consisting ofSEQ ID NOs: 68 to 70, and a recombinant nucleic acid molecule comprisinga promoter operably linked to a second polynucleotide encoding abHLH-like transcription factor polypeptide having at least 95% sequenceidentity to a sequence selected from the group consisting of SEQ ID NOs:5 and 6, wherein said decreased amount is compared to an unmodifiedcontrol tobacco plant.
 23. The cured tobacco leaf of claim 22, whereinsaid Chorismate Mutase-like polypeptide has at least 99% sequenceidentity to a sequence selected from the group consisting of SEQ ID NOs:68 to
 70. 24. The cured tobacco leaf of claim 23, wherein said bHLH-liketranscription factor polypeptide has at least 99% sequence identity to asequence selected from the group consisting of SEQ ID NOs: 5 and
 6. 25.The cured tobacco leaf of claim 22, wherein the amount of said one ormore TSNAs is reduced by at least 50% compared to a cured tobacco leafor a tobacco product from an unmodified control tobacco plant.
 26. Thecured tobacco leaf of claim 22, wherein said cured tobacco leafcomprises less than 0.08 ppm4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), wherein the levelof NNK is measured based on a freeze-dried cured leaf sample usingliquid chromatograph with tandem mass spectrometry (LC/MS/MS).
 27. Atobacco product comprising the cured tobacco leaf of claim
 22. 28. Thetobacco product of claim 27, wherein said tobacco product is selectedfrom the group consisting of a cigarillo, a non-ventilated recess filtercigarette, a vented recess filter cigarette, a cigar, snuff, pipetobacco, cigar tobacco, cigarette tobacco, chewing tobacco, leaftobacco, hookah tobacco, shredded tobacco, cut tobacco, loose leafchewing tobacco, plug chewing tobacco, moist snuff, and nasal snuff. 29.The cured tobacco leaf of claim 22, further comprising a reduced amountof total alkaloids that is a least 10% less than the total amount ofalkaloids in an unmodified control tobacco plant.
 30. The cured tobaccoleaf of claim 22, wherein said cured tobacco leaf comprises less than 2ppm total TSNAs.
 31. The cured tobacco leaf of claim 22, wherein saidone or more tobacco-specific nitrosamines (TSNAs) are selected from thegroup consisting of N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) N′-nitrosoanabasine (NAB), and any combination thereof.
 32. Acured tobacco leaf of a modified tobacco plant, wherein said curedtobacco leaf comprises a decreased amount of one or more tobaccospecific nitrosamines (TSNAs), a recombinant nucleic acid moleculecomprising a promoter operably linked to a first polynucleotide encodingan arogenate dehydrogenase-like polypeptide having at least 95% sequenceidentity to a sequence selected from the group consisting of SEQ ID NOs:51 and 52, and a recombinant nucleic acid molecule comprising a promoteroperably linked to a second polynucleotide encoding a MYB3-liketranscription factor polypeptide having at least 95% sequence identityto a sequence selected from the group consisting of SEQ ID NOs: 13 and23, wherein said decreased amount is compared to an unmodified controltobacco plant.
 33. The cured tobacco leaf of claim 32, wherein saidarogenate dehydrogenase-like polypeptide has at least 99% sequenceidentity to a sequence selected from the group consisting of SEQ ID NOs:51 and
 52. 34. The cured tobacco leaf of claim 33, wherein saidMYB3-like transcription factor polypeptide has at least 99% sequenceidentity to a sequence selected from the group consisting of SEQ ID NOs:13 and
 23. 35. The cured tobacco leaf of claim 32, wherein the amount ofsaid one or more TSNAs is reduced by at least 50% compared to a curedtobacco leaf or a tobacco product from an unmodified control tobaccoplant.
 36. The cured tobacco leaf of claim 32, wherein said curedtobacco leaf comprises less than 0.08 ppm4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), wherein the levelof NNK is measured based on a freeze-dried cured leaf sample usingliquid chromatograph with tandem mass spectrometry (LC/MS/MS).
 37. Atobacco product comprising the cured tobacco leaf of claim
 32. 38. Thetobacco product of claim 37, wherein said tobacco product is selectedfrom the group consisting of a cigarillo, a non-ventilated recess filtercigarette, a vented recess filter cigarette, a cigar, snuff, pipetobacco, cigar tobacco, cigarette tobacco, chewing tobacco, leaftobacco, hookah tobacco, shredded tobacco, cut tobacco, loose leafchewing tobacco, plug chewing tobacco, moist snuff, and nasal snuff. 39.The cured tobacco leaf of claim 32, further comprising a reduced amountof total alkaloids that is a least 10% less than the total amount ofalkaloids in an unmodified control tobacco plant.
 40. The cured tobaccoleaf of claim 32, wherein said cured tobacco leaf comprises less than 2ppm total TSNAs.
 41. The cured tobacco leaf of claim 32, wherein saidone or more tobacco-specific nitrosamines (TSNAs) are selected from thegroup consisting of N′-nitrosonornicotine (NNN),4-methylnitrosoamino-1-(3-pyridyl)-1-butanone (NNK), N′-nitrosoanatabine(NAT) N′-nitrosoanabasine (NAB), and any combination thereof.